-- dump date 20140619_113510 -- class Genbank::misc_feature -- table misc_feature_note -- id note 907238000001 Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus...; Region: Terminator_NusB; cd00619 907238000002 putative RNA binding site [nucleotide binding]; other site 907238000003 lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I; Region: Lumazine_synthase-I; cd09209 907238000004 homopentamer interface [polypeptide binding]; other site 907238000005 active site 907238000006 DAHP synthetase I family; Region: DAHP_synth_1; pfam00793 907238000007 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional; Region: PRK05198 907238000008 Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an...; Region: beta_CA_cladeB; cd00884 907238000009 active site clefts [active] 907238000010 zinc binding site [ion binding]; other site 907238000011 dimer interface [polypeptide binding]; other site 907238000012 Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase...; Region: OMP_decarboxylase_like; cd04725 907238000013 active site 907238000014 dimer interface [polypeptide binding]; other site 907238000015 pantoate--beta-alanine ligase; Region: panC; TIGR00018 907238000016 Pantoate-beta-alanine ligase; Region: PanC; cd00560 907238000017 active site 907238000018 ATP-binding site [chemical binding]; other site 907238000019 pantoate-binding site; other site 907238000020 HXXH motif; other site 907238000021 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000022 chaperonin GroEL; Reviewed; Region: groEL; PRK12849 907238000023 GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found...; Region: GroEL; cd03344 907238000024 ring oligomerisation interface [polypeptide binding]; other site 907238000025 ATP/Mg binding site [chemical binding]; other site 907238000026 stacking interactions; other site 907238000027 hinge regions; other site 907238000028 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It...; Region: cpn10; cd00320 907238000029 oligomerisation interface [polypeptide binding]; other site 907238000030 mobile loop; other site 907238000031 roof hairpin; other site 907238000032 DNA primase, catalytic core; Region: dnaG; TIGR01391 907238000033 CHC2 zinc finger; Region: zf-CHC2; pfam01807 907238000034 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 907238000035 TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG...; Region: TOPRIM_DnaG_primases; cd03364 907238000036 active site 907238000037 metal binding site [ion binding]; metal-binding site 907238000038 interdomain interaction site; other site 907238000039 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]; Region: TrmU; COG0482 907238000040 ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. It belongs to the Adenosine Nucleotide Hydrolysis suoerfamily and predicted to bind to Adenosine nucleotide; Region: ThiI; cd01712 907238000041 Ligand Binding Site [chemical binding]; other site 907238000042 TrbC/VIRB2 family; Region: TrbC; cl01583 907238000043 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 907238000044 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 907238000045 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 907238000046 Walker A motif; other site 907238000047 ATP binding site [chemical binding]; other site 907238000048 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 907238000049 Walker B motif; other site 907238000050 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3014 907238000051 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 907238000052 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907238000053 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238000054 active site 907238000055 phosphorylation site [posttranslational modification] 907238000056 intermolecular recognition site; other site 907238000057 dimerization interface [polypeptide binding]; other site 907238000058 carboxynorspermidine decarboxylase; Region: nspC; TIGR01047 907238000059 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase; Region: PLPDE_III_CANSDC; cd06829 907238000060 dimer interface [polypeptide binding]; other site 907238000061 active site 907238000062 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907238000063 catalytic residues [active] 907238000064 substrate binding site [chemical binding]; other site 907238000065 lipid A 1-phosphatase; Reviewed; Region: PRK09597 907238000066 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 907238000067 active site 907238000068 lipid A phosphoethanolamine transferase; Reviewed; Region: PRK09598 907238000069 Domain of unknown function (DUF1705); Region: DUF1705; pfam08019 907238000070 Sulfatase; Region: Sulfatase; pfam00884 907238000071 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000072 Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS...; Region: EcCS_like; cd06114 907238000073 Citrate synthase [Energy production and conversion]; Region: GltA; COG0372 907238000074 dimer interface [polypeptide binding]; other site 907238000075 active site 907238000076 citrylCoA binding site [chemical binding]; other site 907238000077 NADH binding [chemical binding]; other site 907238000078 cationic pore residues; other site 907238000079 oxalacetate/citrate binding site [chemical binding]; other site 907238000080 coenzyme A binding site [chemical binding]; other site 907238000081 catalytic triad [active] 907238000082 isocitrate dehydrogenase; Validated; Region: PRK07362 907238000083 isocitrate dehydrogenase; Reviewed; Region: PRK07006 907238000084 Protein of unknown function (DUF1523); Region: DUF1523; pfam07509 907238000085 Dethiobiotin synthetase [Coenzyme metabolism]; Region: BioD; COG0132 907238000086 AAA domain; Region: AAA_26; pfam13500 907238000087 Usp: Universal stress protein family. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to...; Region: USP_Like; cd00293 907238000088 Ligand Binding Site [chemical binding]; other site 907238000089 Uncharacterized conserved protein [Function unknown]; Region: COG2127 907238000090 ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]; Region: clpA; COG0542 907238000091 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238000092 Walker A motif; other site 907238000093 ATP binding site [chemical binding]; other site 907238000094 Walker B motif; other site 907238000095 arginine finger; other site 907238000096 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238000097 Walker A motif; other site 907238000098 ATP binding site [chemical binding]; other site 907238000099 Walker B motif; other site 907238000100 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 907238000101 Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production; Region: Asp_decarbox; cd06919 907238000102 tetramerization interface [polypeptide binding]; other site 907238000103 active site 907238000104 hypothetical protein; Provisional; Region: PRK03762 907238000105 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 907238000106 protein binding site [polypeptide binding]; other site 907238000107 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 907238000108 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 907238000109 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 907238000110 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 907238000111 VirB7 interaction site; other site 907238000112 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 907238000113 GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose; Region: GDP-M1P_Guanylyltransferase; cd02509 907238000114 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase; Region: GMP_PMI; TIGR01479 907238000115 Substrate binding site; other site 907238000116 Cupin domain; Region: Cupin_2; cl17218 907238000117 GDP-mannose 4,6-dehydratase; Region: gmd; TIGR01472 907238000118 GDP-mannose 4,6 dehydratase, extended (e) SDRs; Region: GDP_MD_SDR_e; cd05260 907238000119 NADP-binding site; other site 907238000120 homotetramer interface [polypeptide binding]; other site 907238000121 substrate binding site [chemical binding]; other site 907238000122 homodimer interface [polypeptide binding]; other site 907238000123 active site 907238000124 GDP-fucose synthetase, extended (e) SDRs; Region: GDP_FS_SDR_e; cd05239 907238000125 GDP-4-keto-6-deoxymannose-3, 5-epimerase-4-reductase; Region: PLN02725 907238000126 NADP binding site [chemical binding]; other site 907238000127 active site 907238000128 putative substrate binding site [chemical binding]; other site 907238000129 HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the...; Region: HypE; cd02197 907238000130 dimerization interface [polypeptide binding]; other site 907238000131 hydrogenase expression/formation protein HypE; Region: hypE; TIGR02124 907238000132 ATP binding site [chemical binding]; other site 907238000133 Acylphosphatase; Region: Acylphosphatase; pfam00708 907238000134 [NiFe] hydrogenase maturation protein HypF; Region: hypF; TIGR00143 907238000135 HypF finger; Region: zf-HYPF; pfam07503 907238000136 HypF finger; Region: zf-HYPF; pfam07503 907238000137 Telomere recombination; Region: Sua5_yciO_yrdC; pfam01300 907238000138 Peptidylarginine deiminase and related enzymes [Amino acid transport and metabolism]; Region: COG2957 907238000139 Porphyromonas-type peptidyl-arginine deiminase; Region: PAD_porph; pfam04371 907238000140 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907238000141 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238000142 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 907238000143 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 907238000144 cofactor binding site; other site 907238000145 Predicted symporter [General function prediction only]; Region: DhlC; COG4147 907238000146 Na(+)/proline cotransporter PutP and related proteins; solute binding domain; Region: SLC5sbd_PutP; cd11475 907238000147 Na binding site [ion binding]; other site 907238000148 Proline dehydrogenase; Region: Pro_dh; pfam01619 907238000149 Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA; Region: ALDH_PutA-P5CDH; cd07125 907238000150 Aldehyde dehydrogenase family; Region: Aldedh; pfam00171 907238000151 Glutamate binding site [chemical binding]; other site 907238000152 NAD binding site [chemical binding]; other site 907238000153 catalytic residues [active] 907238000154 SH3 domain protein; Region: SH3_and_anchor; TIGR04211 907238000155 Phosphoenolpyruvate carboxylase; Region: PEPcase; cl17418 907238000156 A nuclease of the HNH/ENDO VII superfamily with conserved WHH; Region: WHH; pfam14414 907238000157 SMI1 / KNR4 family; Region: SMI1_KNR4; smart00860 907238000158 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 907238000159 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 907238000160 Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]; Region: UreH; COG0829 907238000161 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cd00882 907238000162 G1 box; other site 907238000163 GTP/Mg2+ binding site [chemical binding]; other site 907238000164 G2 box; other site 907238000165 Switch I region; other site 907238000166 G3 box; other site 907238000167 Switch II region; other site 907238000168 G4 box; other site 907238000169 G5 box; other site 907238000170 Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]; Region: UreF; COG0830 907238000171 UreF; Region: UreF; pfam01730 907238000172 urease accessory protein UreE; Provisional; Region: ureE; PRK13261 907238000173 UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The...; Region: UreE; cd00571 907238000174 dimer interface [polypeptide binding]; other site 907238000175 catalytic residues [active] 907238000176 AmiS/UreI family transporter; Region: AmiS_UreI; pfam02293 907238000177 urease subunit beta; Provisional; Region: ureB; PRK13985 907238000178 Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of...; Region: Urease_alpha; cd00375 907238000179 subunit interactions [polypeptide binding]; other site 907238000180 active site 907238000181 flap region; other site 907238000182 urease subunit alpha; Provisional; Region: PRK13986 907238000183 Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use...; Region: Urease_gamma; cd00390 907238000184 alpha-gamma subunit interface [polypeptide binding]; other site 907238000185 beta-gamma subunit interface [polypeptide binding]; other site 907238000186 Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of...; Region: Urease_beta; cd00407 907238000187 gamma-beta subunit interface [polypeptide binding]; other site 907238000188 alpha-beta subunit interface [polypeptide binding]; other site 907238000189 Signal peptidase (SPase) II; Region: Peptidase_A8; cl00458 907238000190 phosphoglucosamine mutase; Provisional; Region: glmM; PRK14324 907238000191 GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of...; Region: GlmM; cd05802 907238000192 active site 907238000193 substrate binding site [chemical binding]; other site 907238000194 metal binding site [ion binding]; metal-binding site 907238000195 30S ribosomal protein S20; Reviewed; Region: rpsT; PRK00239 907238000196 peptide chain release factor 1; Validated; Region: prfA; PRK00591 907238000197 This domain is found in peptide chain release factors; Region: PCRF; smart00937 907238000198 RF-1 domain; Region: RF-1; pfam00472 907238000199 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000200 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907238000201 dimer interface [polypeptide binding]; other site 907238000202 putative CheW interface [polypeptide binding]; other site 907238000203 30S ribosomal protein S9; Reviewed; Region: rpsI; PRK00132 907238000204 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the...; Region: Ribosomal_L13; cd00392 907238000205 23S rRNA interface [nucleotide binding]; other site 907238000206 L3 interface [polypeptide binding]; other site 907238000207 Malate:quinone oxidoreductase (Mqo); Region: Mqo; cl17341 907238000208 Predicted dehydrogenase [General function prediction only]; Region: COG0579 907238000209 NLPC_P60 stabilising domain, N term; Region: N_NLPC_P60; pfam12912 907238000210 SH3 domain of the SH3b1 type; Region: SH3_6; pfam12913 907238000211 SH3 domain of SH3b2 type; Region: SH3_7; pfam12914 907238000212 Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]; Region: Spr; COG0791 907238000213 NlpC/P60 family; Region: NLPC_P60; pfam00877 907238000214 RNA polymerase sigma factor RpoD; Validated; Region: PRK05658 907238000215 Sigma-70 factor, region 1.2; Region: Sigma70_r1_2; pfam00140 907238000216 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 907238000217 Sigma-70 region 3; Region: Sigma70_r3; pfam04539 907238000218 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 907238000219 DNA binding residues [nucleotide binding] 907238000220 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Region: MTA/SAH-Nsdase; TIGR01704 907238000221 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated; Region: PRK05584 907238000222 (acyl-carrier-protein) S-malonyltransferase [Lipid metabolism]; Region: FabD; COG0331 907238000223 malonyl CoA-acyl carrier protein transacylase; Region: fabD; TIGR00128 907238000224 potential protein location (hypothetical protein HPIN_00430 [Helicobacter pylori India7]) that overlaps RNA (tRNA-S) 907238000225 DpnII restriction endonuclease; Region: DpnII; pfam04556 907238000226 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907238000227 Methyltransferase domain; Region: Methyltransf_26; pfam13659 907238000228 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238000229 potential frameshift: common BLAST hit: gi|108562519|ref|YP_626835.1| alpha-1,2-fucosyltransferase 907238000230 2-hydroxyacid dehydrogenase; Provisional; Region: PRK08410 907238000231 Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; Region: FDH_GDH_like; cl17240 907238000232 NAD binding site [chemical binding]; other site 907238000233 Threonine synthase [Amino acid transport and metabolism]; Region: ThrC; COG0498 907238000234 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants; Region: Thr-synth_2; cd01560 907238000235 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238000236 catalytic residue [active] 907238000237 Methyl-accepting chemotaxis protein [Cell motility and secretion / Signal transduction mechanisms]; Region: Tar; COG0840 907238000238 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907238000239 dimer interface [polypeptide binding]; other site 907238000240 putative CheW interface [polypeptide binding]; other site 907238000241 Adenine nucleotide alpha hydrolases superfamily including N type ATP PPases and ATP sulphurylases. The domain forms a apha/beta/apha fold which binds to Adenosine group; Region: Alpha_ANH_like; cd01986 907238000242 Ligand Binding Site [chemical binding]; other site 907238000243 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000244 Glycosyltransferases involved in cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WcaA; COG0463 907238000245 WfgS and WfeV are involved in O-antigen biosynthesis; Region: GT_2_WfgS_like; cd06433 907238000246 metal-binding site 907238000247 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins; Region: Cache_2; smart01049 907238000248 Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices...; Region: HAMP; cd06225 907238000249 dimerization interface [polypeptide binding]; other site 907238000250 Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer); Region: MA; smart00283 907238000251 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907238000252 dimer interface [polypeptide binding]; other site 907238000253 putative CheW interface [polypeptide binding]; other site 907238000254 5'-nucleotidase/2',3'-cyclic phosphodiesterase and related esterases [Nucleotide transport and metabolism]; Region: UshA; COG0737 907238000255 Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain; Region: MPP_CpdB_N; cd07410 907238000256 active site 907238000257 metal binding site [ion binding]; metal-binding site 907238000258 5'-nucleotidase, C-terminal domain; Region: 5_nucleotid_C; pfam02872 907238000259 S-ribosylhomocysteinase; Provisional; Region: PRK02260 907238000260 cystathionine gamma-synthase/cystathionine beta-lyase; Validated; Region: PRK06176 907238000261 CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of...; Region: CGS_like; cd00614 907238000262 homodimer interface [polypeptide binding]; other site 907238000263 substrate-cofactor binding pocket; other site 907238000264 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238000265 catalytic residue [active] 907238000266 Cysteine synthase [Amino acid transport and metabolism]; Region: CysK; COG0031 907238000267 CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine; Region: CBS_like; cd01561 907238000268 dimer interface [polypeptide binding]; other site 907238000269 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238000270 catalytic residue [active] 907238000271 molecular chaperone DnaK; Provisional; Region: dnaK; PRK00290 907238000272 Nucleotide-binding domain of human HSPA9 and similar proteins; Region: HSPA9-Ssq1-like_NBD; cd10234 907238000273 nucleotide binding site [chemical binding]; other site 907238000274 NEF interaction site [polypeptide binding]; other site 907238000275 SBD interface [polypeptide binding]; other site 907238000276 Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]; Region: GrpE; COG0576 907238000277 GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding; Region: GrpE; cd00446 907238000278 dimer interface [polypeptide binding]; other site 907238000279 hsp70 (ATPase domain) interactions [polypeptide binding]; other site 907238000280 heat-inducible transcription repressor; Provisional; Region: PRK03911 907238000281 hypothetical protein; Provisional; Region: PRK05834 907238000282 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 907238000283 flagellin B; Provisional; Region: PRK13588 907238000284 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 907238000285 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907238000286 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907238000287 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 907238000288 DNA topoisomerase I; Validated; Region: PRK05582 907238000289 TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the...; Region: TOPRIM_TopoIA_TopoI; cd03363 907238000290 active site 907238000291 interdomain interaction site; other site 907238000292 putative metal-binding site [ion binding]; other site 907238000293 nucleotide binding site [chemical binding]; other site 907238000294 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 907238000295 domain I; other site 907238000296 DNA binding groove [nucleotide binding] 907238000297 phosphate binding site [ion binding]; other site 907238000298 domain II; other site 907238000299 domain III; other site 907238000300 nucleotide binding site [chemical binding]; other site 907238000301 catalytic site [active] 907238000302 domain IV; other site 907238000303 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 907238000304 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 907238000305 Topoisomerase DNA binding C4 zinc finger; Region: zf-C4_Topoisom; pfam01396 907238000306 Fe-S oxidoreductases [Energy production and conversion]; Region: COG0731 907238000307 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238000308 FeS/SAM binding site; other site 907238000309 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 907238000310 phosphoenolpyruvate synthase; Validated; Region: PRK06464 907238000311 Pyruvate phosphate dikinase, PEP/pyruvate binding domain; Region: PPDK_N; pfam01326 907238000312 PEP-utilising enzyme, mobile domain; Region: PEP-utilizers; pfam00391 907238000313 PEP-utilising enzyme, TIM barrel domain; Region: PEP-utilizers_C; pfam02896 907238000314 threonyl-tRNA synthetase; Reviewed; Region: thrS; PRK12305 907238000315 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; pfam07973 907238000316 Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ThrRS_core; cd00771 907238000317 active site 907238000318 dimer interface [polypeptide binding]; other site 907238000319 motif 1; other site 907238000320 motif 2; other site 907238000321 motif 3; other site 907238000322 ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: ThrRS_anticodon; cd00860 907238000323 anticodon binding site; other site 907238000324 Translation initiation factor IF-3, N-terminal domain; Region: IF3_N; pfam05198 907238000325 translation initiation factor IF-3; Region: infC; TIGR00168 907238000326 Translation initiation factor IF-3, C-terminal domain; Region: IF3_C; pfam00707 907238000327 50S ribosomal protein L35; Reviewed; Region: rpmI; PRK00172 907238000328 Ribosomal protein L20; Region: Ribosomal_L20; cd07026 907238000329 23S rRNA binding site [nucleotide binding]; other site 907238000330 L21 binding site [polypeptide binding]; other site 907238000331 L13 binding site [polypeptide binding]; other site 907238000332 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000333 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 907238000334 L-serine dehydratase, iron-sulfur-dependent, single chain form; Region: sda_mono; TIGR00720 907238000335 Serine dehydratase beta chain; Region: SDH_beta; pfam03315 907238000336 Serine dehydratase alpha chain; Region: SDH_alpha; pfam03313 907238000337 Amino acid permeases [Amino acid transport and metabolism]; Region: SdaC; COG0814 907238000338 serine transporter; Region: stp; TIGR00814 907238000339 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]; Region: AroG; COG3200 907238000340 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 907238000341 Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing...; Region: PRX_BCP; cd03017 907238000342 catalytic triad [active] 907238000343 Uncharacterized conserved protein [Function unknown]; Region: COG1556 907238000344 iron-sulfur cluster-binding protein; Region: TIGR00273 907238000345 Uncharacterized ACR, YkgG family COG1556; Region: DUF162; pfam02589 907238000346 Domain of unknown function (DUF3390); Region: DUF3390; pfam11870 907238000347 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 907238000348 Cysteine-rich domain; Region: CCG; pfam02754 907238000349 Cysteine-rich domain; Region: CCG; pfam02754 907238000350 L-lactate transport; Region: lctP; TIGR00795 907238000351 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 907238000352 L-lactate permease [Energy production and conversion]; Region: LldP; COG1620 907238000353 L-lactate transport; Region: lctP; TIGR00795 907238000354 DNA glycosylase MutY; Provisional; Region: PRK13910 907238000355 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 907238000356 minor groove reading motif; other site 907238000357 helix-hairpin-helix signature motif; other site 907238000358 substrate binding pocket [chemical binding]; other site 907238000359 active site 907238000360 DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the Nudix hydrolase superfamily and is important...; Region: DNA_Glycosylase_C; cd03431 907238000361 DNA binding and oxoG recognition site [nucleotide binding] 907238000362 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 907238000363 Sodium:sulfate symporter transmembrane region; Region: Na_sulph_symp; pfam00939 907238000364 transmembrane helices; other site 907238000365 Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is...; Region: Heme_Cu_Oxidase_I; cl00275 907238000366 Low-spin heme binding site [chemical binding]; other site 907238000367 Cytochrome C and Quinol oxidase polypeptide I; Region: COX1; pfam00115 907238000368 D-pathway; other site 907238000369 Putative water exit pathway; other site 907238000370 Binuclear center (active site) [active] 907238000371 K-pathway; other site 907238000372 Putative proton exit pathway; other site 907238000373 Cbb3-type cytochrome oxidase, cytochrome c subunit [Energy production and conversion]; Region: CcoO; COG2993 907238000374 Cytochrome C oxidase, mono-heme subunit/FixO; Region: FixO; cl01130 907238000375 cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial; Region: cbb3_Q_epsi; TIGR02736 907238000376 cytochrome c oxidase, cbb3-type, subunit III; Region: ccoP; TIGR00782 907238000377 Cytochrome c; Region: Cytochrom_C; pfam00034 907238000378 Cytochrome c; Region: Cytochrom_C; pfam00034 907238000379 Family of unknown function (DUF4006); Region: DUF4006; pfam13179 907238000380 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG2107 907238000381 recombinase A; Provisional; Region: recA; PRK09354 907238000382 RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange; Region: recA; cd00983 907238000383 hexamer interface [polypeptide binding]; other site 907238000384 Walker A motif; other site 907238000385 ATP binding site [chemical binding]; other site 907238000386 Walker B motif; other site 907238000387 enolase; Provisional; Region: eno; PRK00077 907238000388 Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions; Region: enolase; cd03313 907238000389 dimer interface [polypeptide binding]; other site 907238000390 metal binding site [ion binding]; metal-binding site 907238000391 substrate binding pocket [chemical binding]; other site 907238000392 AMIN domain; Region: AMIN; pfam11741 907238000393 Shikimate kinase [Amino acid transport and metabolism]; Region: AroK; COG0703 907238000394 Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis...; Region: SK; cd00464 907238000395 ADP binding site [chemical binding]; other site 907238000396 magnesium binding site [ion binding]; other site 907238000397 putative shikimate binding site; other site 907238000398 Cache domain; Region: Cache_1; pfam02743 907238000399 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907238000400 A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface; Region: GT8_A4GalT_like; cd04194 907238000401 Ligand binding site; other site 907238000402 metal-binding site 907238000403 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907238000404 Sel1-like repeats; Region: SEL1; smart00671 907238000405 Sel1-like repeats; Region: SEL1; smart00671 907238000406 Sel1-like repeats; Region: SEL1; smart00671 907238000407 Sel1-like repeats; Region: SEL1; smart00671 907238000408 Sel1-like repeats; Region: SEL1; smart00671 907238000409 Sel1-like repeats; Region: SEL1; smart00671 907238000410 hypothetical protein; Provisional; Region: PRK12378 907238000411 Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the...; Region: ALAD_PBGS; cd00384 907238000412 dimer interface [polypeptide binding]; other site 907238000413 active site 907238000414 Schiff base residues; other site 907238000415 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 907238000416 HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain; Region: HAMP; smart00304 907238000417 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 907238000418 dimer interface [polypeptide binding]; other site 907238000419 phosphorylation site [posttranslational modification] 907238000420 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 907238000421 ATP binding site [chemical binding]; other site 907238000422 Mg2+ binding site [ion binding]; other site 907238000423 G-X-G motif; other site 907238000424 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 907238000425 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238000426 active site 907238000427 phosphorylation site [posttranslational modification] 907238000428 intermolecular recognition site; other site 907238000429 dimerization interface [polypeptide binding]; other site 907238000430 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 907238000431 DNA binding site [nucleotide binding] 907238000432 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cl02429 907238000433 Collagenase and related proteases [Posttranslational modification, protein turnover, chaperones]; Region: COG0826 907238000434 Peptidase family U32; Region: Peptidase_U32; pfam01136 907238000435 peptide chain release factor 2; Region: prfB; TIGR00020 907238000436 This domain is found in peptide chain release factors; Region: PCRF; smart00937 907238000437 RF-1 domain; Region: RF-1; pfam00472 907238000438 Molybdopterin biosynthesis enzyme [Coenzyme metabolism]; Region: MoeA; COG0303 907238000439 MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoeA; cd00887 907238000440 dimer interface [polypeptide binding]; other site 907238000441 putative functional site; other site 907238000442 putative MPT binding site; other site 907238000443 Flagellar biosynthesis pathway, component FliR [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FliR; COG1684 907238000444 Etoposide-induced protein 2.4 (EI24); Region: EI24; pfam07264 907238000445 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 907238000446 PPIC-type PPIASE domain; Region: Rotamase; pfam00639 907238000447 fructose-bisphosphate aldolase; Provisional; Region: PRK09197 907238000448 Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1; Region: TBP_aldolase_IIB; cd00947 907238000449 intersubunit interface [polypeptide binding]; other site 907238000450 active site 907238000451 zinc binding site [ion binding]; other site 907238000452 Na+ binding site [ion binding]; other site 907238000453 elongation factor P; Validated; Region: PRK00529 907238000454 Elongation factor P (EF-P) KOW-like domain; Region: EFP_N; pfam08207 907238000455 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_1; cd04470 907238000456 RNA binding site [nucleotide binding]; other site 907238000457 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with...; Region: S1_EF-P_repeat_2; cd05794 907238000458 RNA binding site [nucleotide binding]; other site 907238000459 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]; Region: COG1942 907238000460 active site 1 [active] 907238000461 dimer interface [polypeptide binding]; other site 907238000462 hexamer interface [polypeptide binding]; other site 907238000463 active site 2 [active] 907238000464 Fic family protein [Function unknown]; Region: COG3177 907238000465 Fic/DOC family; Region: Fic; pfam02661 907238000466 Initiator Replication protein; Region: Rep_3; cl17676 907238000467 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238000468 heat shock protein 90; Provisional; Region: PRK05218 907238000469 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 907238000470 ATP binding site [chemical binding]; other site 907238000471 Mg2+ binding site [ion binding]; other site 907238000472 G-X-G motif; other site 907238000473 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907238000474 Sel1-like repeats; Region: SEL1; smart00671 907238000475 Sel1-like repeats; Region: SEL1; smart00671 907238000476 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 907238000477 TPR motif; other site 907238000478 binding surface 907238000479 succinyl-diaminopimelate desuccinylase; Reviewed; Region: PRK13009 907238000480 M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase; Region: M20_DapE_proteobac; cd03891 907238000481 metal binding site [ion binding]; metal-binding site 907238000482 dimer interface [polypeptide binding]; other site 907238000483 glucose-inhibited division protein A; Region: gidA; TIGR00136 907238000484 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 907238000485 NAD(FAD)-utilizing enzyme possibly involved in translation [Translation, ribosomal structure and biogenesis]; Region: Gid; COG1206 907238000486 GidA associated domain 3; Region: GIDA_assoc_3; pfam13932 907238000487 Di- and tricarboxylate transporters [Inorganic ion transport and metabolism]; Region: CitT; COG0471 907238000488 Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is...; Region: SLC13_permease; cd01115 907238000489 transmembrane helices; other site 907238000490 CDP-diglyceride synthetase [Lipid metabolism]; Region: CdsA; COG0575 907238000491 Cytidylyltransferase family; Region: CTP_transf_1; pfam01148 907238000492 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: Dxr; TIGR00243 907238000493 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Region: DXP_reductoisom; pfam02670 907238000494 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal; Region: DXP_redisom_C; pfam08436 907238000495 DXP reductoisomerase C-terminal domain; Region: DXPR_C; pfam13288 907238000496 PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea; Region: PEBP_bact_arch; cd00865 907238000497 substrate binding site [chemical binding]; other site 907238000498 Helix-turn-helix domain; Region: HTH_28; pfam13518 907238000499 cysteine desulfurase, NifS family, epsilon proteobacteria type; Region: nifS_epsilon; TIGR03403 907238000500 cysteine desulfurase NifS; Region: FeS_nifS; TIGR03402 907238000501 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 907238000502 catalytic residue [active] 907238000503 Fe-S cluster assembly protein NifU; Region: NifU_proper; TIGR02000 907238000504 Iron-sulfur cluster scaffold-like proteins; Region: IscU_like; cd06664 907238000505 trimerization site [polypeptide binding]; other site 907238000506 active site 907238000507 BFD-like [2Fe-2S] binding domain; Region: Fer2_BFD; pfam04324 907238000508 Thioredoxin-like proteins and domains [Posttranslational modification, protein turnover, chaperones]; Region: COG0694 907238000509 DNA repair protein RadA; Region: sms; TIGR00416 907238000510 Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of...; Region: Sms; cd01121 907238000511 Walker A motif/ATP binding site; other site 907238000512 ATP binding site [chemical binding]; other site 907238000513 Walker B motif; other site 907238000514 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 907238000515 Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: MsrA; COG0225 907238000516 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]; Region: COG0229 907238000517 SelR domain; Region: SelR; pfam01641 907238000518 Predicted permeases [General function prediction only]; Region: COG0730 907238000519 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000520 Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]; Region: SUL1; COG0659 907238000521 Sulfate transporter N-terminal domain with GLY motif; Region: Sulfate_tra_GLY; pfam13792 907238000522 Sulfate transporter family; Region: Sulfate_transp; pfam00916 907238000523 potential protein location (hypothetical protein HPIN_01010 [Helicobacter pylori India7]) that overlaps RNA (tRNA-N) 907238000524 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000525 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional; Region: PRK05450 907238000526 CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide; Region: CMP-KDO-Synthetase; cd02517 907238000527 Ligand binding site; other site 907238000528 oligomer interface; other site 907238000529 Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]; Region: DsbG; COG1651 907238000530 Protein Disulfide Oxidoreductases and Other Proteins with a Thioredoxin fold; Region: Thioredoxin_like; cl00388 907238000531 hypothetical protein; Provisional; Region: PRK04081 907238000532 Glutathionylspermidine synthase [Amino acid transport and metabolism]; Region: Gsp; COG0754 907238000533 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3295 907238000534 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907238000535 Sel1-like repeats; Region: SEL1; smart00671 907238000536 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 907238000537 binding surface 907238000538 TPR motif; other site 907238000539 Sel1-like repeats; Region: SEL1; smart00671 907238000540 Sel1-like repeats; Region: SEL1; smart00671 907238000541 Cytochrome c; Region: Cytochrom_C; cl11414 907238000542 Porphobilinogen deaminase [Coenzyme metabolism]; Region: HemC; COG0181 907238000543 Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12. HMBS catalyzes the conversion of...; Region: HMBS; cd00494 907238000544 domain interfaces; other site 907238000545 active site 907238000546 prolyl-tRNA synthetase, family II; Region: proS_fam_II; TIGR00409 907238000547 Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: ProRS_core_prok; cd00779 907238000548 dimer interface [polypeptide binding]; other site 907238000549 motif 1; other site 907238000550 active site 907238000551 motif 2; other site 907238000552 INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and...; Region: ProRS-INS; cd04334 907238000553 putative deacylase active site [active] 907238000554 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 907238000555 active site 907238000556 motif 3; other site 907238000557 ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding; Region: ProRS_anticodon_short; cd00861 907238000558 anticodon binding site; other site 907238000559 glutamyl-tRNA reductase; Region: hemA; TIGR01035 907238000560 NADP-binding domain of glutamyl-tRNA reductase; Region: NAD_bind_Glutamyl_tRNA_reduct; cd05213 907238000561 tRNA; other site 907238000562 putative tRNA binding site [nucleotide binding]; other site 907238000563 putative NADP binding site [chemical binding]; other site 907238000564 Glutamyl-tRNAGlu reductase, dimerisation domain; Region: GlutR_dimer; pfam00745 907238000565 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 907238000566 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 907238000567 substrate binding pocket [chemical binding]; other site 907238000568 chain length determination region; other site 907238000569 substrate-Mg2+ binding site; other site 907238000570 catalytic residues [active] 907238000571 aspartate-rich region 1; other site 907238000572 active site lid residues [active] 907238000573 aspartate-rich region 2; other site 907238000574 Domain of unknown function (DUF2018); Region: DUF2018; pfam09442 907238000575 DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]; Region: Dps; COG0783 907238000576 DPS protein, ferritin-like diiron-binding domain; Region: DPS; cd01043 907238000577 dimerization interface [polypeptide binding]; other site 907238000578 DPS ferroxidase diiron center [ion binding]; other site 907238000579 ion pore; other site 907238000580 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 907238000581 Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via...; Region: HisKA; cd00082 907238000582 dimer interface [polypeptide binding]; other site 907238000583 phosphorylation site [posttranslational modification] 907238000584 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 907238000585 ATP binding site [chemical binding]; other site 907238000586 Mg2+ binding site [ion binding]; other site 907238000587 G-X-G motif; other site 907238000588 flagellar basal body P-ring protein; Provisional; Region: flgI; PRK05303 907238000589 flagellar basal body P-ring protein; Reviewed; Region: flgI; cl14622 907238000590 Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]; Region: SrmB; COG0513 907238000591 DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif; Region: DEADc; cd00268 907238000592 ATP binding site [chemical binding]; other site 907238000593 Mg++ binding site [ion binding]; other site 907238000594 motif III; other site 907238000595 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 907238000596 nucleotide binding region [chemical binding]; other site 907238000597 ATP-binding site [chemical binding]; other site 907238000598 Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]; Region: HflC; COG0330 907238000599 SPFH domain / Band 7 family; Region: Band_7; pfam01145 907238000600 Protein of unknown function (DUF2393); Region: DUF2393; pfam09624 907238000601 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]; Region: COG1123 907238000602 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907238000603 Walker A/P-loop; other site 907238000604 ATP binding site [chemical binding]; other site 907238000605 Q-loop/lid; other site 907238000606 ABC transporter signature motif; other site 907238000607 Walker B; other site 907238000608 D-loop; other site 907238000609 H-loop/switch region; other site 907238000610 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 907238000611 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907238000612 Walker A/P-loop; other site 907238000613 ATP binding site [chemical binding]; other site 907238000614 Q-loop/lid; other site 907238000615 ABC transporter signature motif; other site 907238000616 Walker B; other site 907238000617 D-loop; other site 907238000618 H-loop/switch region; other site 907238000619 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 907238000620 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4239 907238000621 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238000622 dimer interface [polypeptide binding]; other site 907238000623 conserved gate region; other site 907238000624 putative PBP binding loops; other site 907238000625 ABC-ATPase subunit interface; other site 907238000626 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000627 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000628 Adenylosuccinate synthetase; Region: Adenylsucc_synt; smart00788 907238000629 Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the...; Region: AdSS; cd03108 907238000630 GDP-binding site [chemical binding]; other site 907238000631 ACT binding site; other site 907238000632 IMP binding site; other site 907238000633 Flagellar FliJ protein; Region: FliJ; pfam02050 907238000634 Uncharacterized conserved protein [Function unknown]; Region: COG3334 907238000635 RIP metalloprotease RseP; Region: TIGR00054 907238000636 RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog...; Region: S2P-M50_PDZ_RseP-like; cd06163 907238000637 active site 907238000638 PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ...; Region: PDZ_metalloprotease; cd00989 907238000639 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic...; Region: S2P-M50; cl10020 907238000640 putative substrate binding region [chemical binding]; other site 907238000641 exodeoxyribonuclease VII, large subunit; Region: xseA; TIGR00237 907238000642 ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a...; Region: ExoVII_LU_OBF; cd04489 907238000643 generic binding surface II; other site 907238000644 generic binding surface I; other site 907238000645 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907238000646 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238000647 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238000648 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907238000649 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238000650 ATP-dependent chaperone ClpB; Region: chaperone_ClpB; TIGR03346 907238000651 Clp amino terminal domain; Region: Clp_N; pfam02861 907238000652 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238000653 Walker A motif; other site 907238000654 ATP binding site [chemical binding]; other site 907238000655 Walker B motif; other site 907238000656 arginine finger; other site 907238000657 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238000658 Walker A motif; other site 907238000659 ATP binding site [chemical binding]; other site 907238000660 Walker B motif; other site 907238000661 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; pfam10431 907238000662 Cytochrome c biogenesis protein [Posttranslational modification, protein turnover, chaperones]; Region: CcdA; COG0785 907238000663 Cytochrome C biogenesis protein transmembrane region; Region: DsbD; pfam02683 907238000664 Dihydroorotase and related cyclic amidohydrolases [Nucleotide transport and metabolism]; Region: PyrC; COG0044 907238000665 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 907238000666 Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a...; Region: metallo-dependent_hydrolases; cl00281 907238000667 active site 907238000668 chlorohydrolase; Provisional; Region: PRK08418 907238000669 Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the...; Region: Met_dep_hydrolase_D; cd01312 907238000670 active site 907238000671 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional; Region: PRK14339 907238000672 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 907238000673 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238000674 FeS/SAM binding site; other site 907238000675 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374; Region: LPLAT_DUF374-like; cd07983 907238000676 putative acyl-acceptor binding pocket; other site 907238000677 Predicted Fe-S-cluster oxidoreductase [General function prediction only]; Region: COG0727 907238000678 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 907238000679 4Fe-4S dicluster domain; Region: Fer4_7; pfam12838 907238000680 Exopolyphosphatase [Nucleotide transport and metabolism / Inorganic ion transport and metabolism]; Region: GppA; COG0248 907238000681 Ppx/GppA phosphatase family; Region: Ppx-GppA; pfam02541 907238000682 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907238000683 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 907238000684 putative active site [active] 907238000685 Bacterial lipid A biosynthesis acyltransferase; Region: Lip_A_acyltrans; pfam03279 907238000686 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like; Region: LPLAT_LABLAT-like; cd07984 907238000687 putative acyl-acceptor binding pocket; other site 907238000688 queuine tRNA-ribosyltransferase; Provisional; Region: tgt; PRK00112 907238000689 tRNA-guanine family transglycosylase; Region: tgt_general; TIGR00449 907238000690 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3400 907238000691 TrkA-C domain; Region: TrkA_C; pfam02080 907238000692 Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis; Region: DHQS; cd08195 907238000693 Glycerol dehydrogenase and related enzymes [Energy production and conversion]; Region: GldA; COG0371 907238000694 active site 907238000695 dimer interface [polypeptide binding]; other site 907238000696 metal binding site [ion binding]; metal-binding site 907238000697 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 907238000698 Mechanosensitive ion channel; Region: MS_channel; pfam00924 907238000699 radical SAM methylthiotransferase, MiaB/RimO family; Region: TIGR00089 907238000700 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 907238000701 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238000702 FeS/SAM binding site; other site 907238000703 ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]; Region: HflB; COG0465 907238000704 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238000705 Walker A motif; other site 907238000706 ATP binding site [chemical binding]; other site 907238000707 Walker B motif; other site 907238000708 arginine finger; other site 907238000709 Domain of unknown function (DUF4149); Region: DUF4149; pfam13664 907238000710 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238000711 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238000712 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907238000713 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238000714 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907238000715 diaminopimelate decarboxylase; Region: lysA; TIGR01048 907238000716 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase; Region: PLPDE_III_DapDC; cd06828 907238000717 active site 907238000718 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907238000719 substrate binding site [chemical binding]; other site 907238000720 catalytic residues [active] 907238000721 dimer interface [polypeptide binding]; other site 907238000722 Chorismate mutase [Amino acid transport and metabolism]; Region: PheA; COG1605 907238000723 Uncharacterized conserved protein [Function unknown]; Region: COG4866 907238000724 aminodeoxychorismate synthase; Provisional; Region: PRK07508 907238000725 chorismate binding enzyme; Region: Chorismate_bind; cl10555 907238000726 PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and...; Region: PLPDE_IV; cl00224 907238000727 Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism / Coenzyme metabolism]; Region: IlvE; COG0115 907238000728 substrate-cofactor binding pocket; other site 907238000729 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238000730 catalytic residue [active] 907238000731 acylamide amidohydrolase; Provisional; Region: amiE; PRK13286 907238000732 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 907238000733 multimer interface [polypeptide binding]; other site 907238000734 active site 907238000735 catalytic triad [active] 907238000736 dimer interface [polypeptide binding]; other site 907238000737 flagellar hook-associated protein FlgL; Validated; Region: flgL; PRK08412 907238000738 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 907238000739 50S ribosomal protein L21; Validated; Region: rplU; PRK05573 907238000740 50S ribosomal protein L27; Validated; Region: rpmA; PRK05435 907238000741 ABC-type dipeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: DdpA; COG0747 907238000742 The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold; Region: PBP2_DppA_like; cd08493 907238000743 peptide binding site [polypeptide binding]; other site 907238000744 ABC-type dipeptide/oligopeptide/nickel transport systems, permease components [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppB; COG0601 907238000745 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238000746 dimer interface [polypeptide binding]; other site 907238000747 conserved gate region; other site 907238000748 putative PBP binding loops; other site 907238000749 ABC-ATPase subunit interface; other site 907238000750 dipeptide transporter; Provisional; Region: PRK10913 907238000751 N-terminal TM domain of oligopeptide transport permease C; Region: OppC_N; pfam12911 907238000752 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238000753 dimer interface [polypeptide binding]; other site 907238000754 conserved gate region; other site 907238000755 putative PBP binding loops; other site 907238000756 ABC-ATPase subunit interface; other site 907238000757 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907238000758 nickel import ATP-binding protein NikD; Region: nickel_nikD; TIGR02770 907238000759 Walker A/P-loop; other site 907238000760 ATP binding site [chemical binding]; other site 907238000761 Q-loop/lid; other site 907238000762 ABC transporter signature motif; other site 907238000763 Walker B; other site 907238000764 D-loop; other site 907238000765 H-loop/switch region; other site 907238000766 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; cl07097 907238000767 ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]; Region: DppF; COG1124 907238000768 ATP-binding cassette domain of nickel/oligopeptides specific transporters; Region: ABC_NikE_OppD_transporters; cd03257 907238000769 Walker A/P-loop; other site 907238000770 ATP binding site [chemical binding]; other site 907238000771 Q-loop/lid; other site 907238000772 ABC transporter signature motif; other site 907238000773 Walker B; other site 907238000774 D-loop; other site 907238000775 H-loop/switch region; other site 907238000776 Oligopeptide/dipeptide transporter, C-terminal region; Region: oligo_HPY; pfam08352 907238000777 GTPase CgtA; Reviewed; Region: obgE; PRK12299 907238000778 GTP1/OBG; Region: GTP1_OBG; pfam01018 907238000779 Obg GTPase; Region: Obg; cd01898 907238000780 G1 box; other site 907238000781 GTP/Mg2+ binding site [chemical binding]; other site 907238000782 Switch I region; other site 907238000783 G2 box; other site 907238000784 G3 box; other site 907238000785 Switch II region; other site 907238000786 G4 box; other site 907238000787 G5 box; other site 907238000788 Alginate lyase; Region: Alginate_lyase; pfam05426 907238000789 glutamate-1-semialdehyde aminotransferase; Provisional; Region: PRK00062 907238000790 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 907238000791 inhibitor-cofactor binding pocket; inhibition site 907238000792 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238000793 catalytic residue [active] 907238000794 Putative F0F1-ATPase subunit (ATPase_gene1); Region: ATPase_gene1; pfam09527 907238000795 Predicted amidohydrolase [General function prediction only]; Region: COG0388 907238000796 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 907238000797 active site 907238000798 catalytic triad [active] 907238000799 dimer interface [polypeptide binding]; other site 907238000800 Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins; Region: CE4_HpPgdA_like; cd10938 907238000801 active site 907238000802 catalytic site [active] 907238000803 Zn binding site [ion binding]; other site 907238000804 tetramer interface [polypeptide binding]; other site 907238000805 Predicted xylanase/chitin deacetylase [Carbohydrate transport and metabolism]; Region: CDA1; COG0726 907238000806 Putative GTPases (G3E family) [General function prediction only]; Region: COG0523 907238000807 CobW/HypB/UreG, nucleotide-binding domain; Region: cobW; pfam02492 907238000808 Cobalamin synthesis protein cobW C-terminal domain; Region: CobW_C; pfam07683 907238000809 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 907238000810 Major Facilitator Superfamily; Region: MFS_1; pfam07690 907238000811 putative substrate translocation pore; other site 907238000812 heme oxygenase, HugZ family; Region: heme_ox_HugZ; TIGR04109 907238000813 Protein of unknown function (DUF2470); Region: DUF2470; pfam10615 907238000814 Pyridoxine 5'-phosphate (PNP) oxidase-like proteins; Region: PNPOx_like; cl00381 907238000815 Arginyl tRNA synthetase N terminal domain; Region: Arg_tRNA_synt_N; pfam03485 907238000816 arginyl-tRNA synthetase; Region: argS; TIGR00456 907238000817 catalytic core domain of arginyl-tRNA synthetases; Region: ArgRS_core; cd00671 907238000818 active site 907238000819 HIGH motif; other site 907238000820 KMSK motif region; other site 907238000821 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 907238000822 tRNA binding surface [nucleotide binding]; other site 907238000823 anticodon binding site; other site 907238000824 mttA/Hcf106 family; Region: MttA_Hcf106; cl00788 907238000825 Guanylate kinase [Nucleotide transport and metabolism]; Region: Gmk; COG0194 907238000826 Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine...; Region: GMPK; cd00071 907238000827 catalytic site [active] 907238000828 G-X2-G-X-G-K; other site 907238000829 Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins; Region: PLDc_Nuc_like; cd09116 907238000830 PLD-like domain; Region: PLDc_2; pfam13091 907238000831 putative active site [active] 907238000832 catalytic site [active] 907238000833 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000834 Flagellar basal body L-ring protein [Cell motility and secretion]; Region: FlgH; COG2063 907238000835 flagellar basal body L-ring protein; Reviewed; Region: flgH; PRK00249 907238000836 CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety; Region: CMP-NeuAc_Synthase; cd02513 907238000837 ligand binding site; other site 907238000838 tetramer interface; other site 907238000839 Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: spsG; COG3980 907238000840 pseudaminic acid biosynthesis N-acetyl transferase; Region: PseH; TIGR03585 907238000841 Acetyltransferase (GNAT) family; Region: Acetyltransf_1; pfam00583 907238000842 Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]; Region: LpxK; COG1663 907238000843 tetraacyldisaccharide 4'-kinase; Reviewed; Region: lpxK; PRK00652 907238000844 NAD synthetase; Provisional; Region: PRK13980 907238000845 NAD+ synthase is a homodimer, which catalyzes the final step in de novo nicotinamide adenine dinucleotide (NAD+) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD...; Region: NAD_synthase; cd00553 907238000846 homodimer interface [polypeptide binding]; other site 907238000847 NAD binding pocket [chemical binding]; other site 907238000848 ATP binding pocket [chemical binding]; other site 907238000849 Mg binding site [ion binding]; other site 907238000850 active-site loop [active] 907238000851 ketol-acid reductoisomerase; Provisional; Region: PRK05479 907238000852 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvN; pfam07991 907238000853 Acetohydroxy acid isomeroreductase, catalytic domain; Region: IlvC; pfam01450 907238000854 Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]; Region: MinD; COG2894 907238000855 Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal...; Region: MinD; cd02036 907238000856 Switch I; other site 907238000857 Switch II; other site 907238000858 cell division topological specificity factor MinE; Region: minE; TIGR01215 907238000859 DNA protecting protein DprA; Region: dprA; TIGR00732 907238000860 Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]; Region: Smf; COG0758 907238000861 Holliday junction resolvase-like protein; Reviewed; Region: PRK00109 907238000862 potential frameshift: common BLAST hit: gi|308182509|ref|YP_003926636.1| cysteine-rich protein H 907238000863 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: FcbT1; COG4663 907238000864 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 907238000865 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 907238000866 active site 907238000867 single-stranded-DNA-specific exonuclease RecJ; Region: recJ; TIGR00644 907238000868 DHH family; Region: DHH; pfam01368 907238000869 DHHA1 domain; Region: DHHA1; pfam02272 907238000870 CTP synthetase; Validated; Region: pyrG; PRK05380 907238000871 CTP synthetase (CTPs) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent...; Region: CTGs; cd03113 907238000872 Catalytic site [active] 907238000873 active site 907238000874 UTP binding site [chemical binding]; other site 907238000875 Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase; Region: GATase1_CTP_Synthase; cd01746 907238000876 active site 907238000877 putative oxyanion hole; other site 907238000878 catalytic triad [active] 907238000879 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 907238000880 active site 907238000881 flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF); Region: fliF; TIGR00206 907238000882 Secretory protein of YscJ/FliF family; Region: YscJ_FliF; pfam01514 907238000883 Flagellar M-ring protein C-terminal; Region: YscJ_FliF_C; pfam08345 907238000884 flagellar motor switch protein FliG; Region: fliG; TIGR00207 907238000885 FliG C-terminal domain; Region: FliG_C; pfam01706 907238000886 flagellar assembly protein H; Validated; Region: fliH; PRK06669 907238000887 Flagellar assembly protein FliH; Region: FliH; pfam02108 907238000888 1-deoxy-D-xylulose-5-phosphate synthase; Region: dxs; TIGR00204 907238000889 Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products...; Region: TPP_DXS; cd02007 907238000890 TPP-binding site; other site 907238000891 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 907238000892 PYR/PP interface [polypeptide binding]; other site 907238000893 dimer interface [polypeptide binding]; other site 907238000894 TPP binding site [chemical binding]; other site 907238000895 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 907238000896 GTP-binding protein LepA; Provisional; Region: PRK05433 907238000897 LepA also known as Elongation Factor 4 (EF4); Region: LepA; cd01890 907238000898 G1 box; other site 907238000899 putative GEF interaction site [polypeptide binding]; other site 907238000900 GTP/Mg2+ binding site [chemical binding]; other site 907238000901 Switch I region; other site 907238000902 G2 box; other site 907238000903 G3 box; other site 907238000904 Switch II region; other site 907238000905 G4 box; other site 907238000906 G5 box; other site 907238000907 Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to...; Region: Translation_Factor_II_like; cl02787 907238000908 lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits...; Region: lepA_C; cd03709 907238000909 GTP-binding protein LepA C-terminus; Region: LepA_C; pfam06421 907238000910 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 907238000911 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 907238000912 cofactor binding site; other site 907238000913 DNA binding site [nucleotide binding] 907238000914 substrate interaction site [chemical binding]; other site 907238000915 Flagellar basal body rod protein [Cell motility and secretion]; Region: FlgG; COG4786 907238000916 flagellar basal-body rod protein FlgF; Region: flgF; TIGR02490 907238000917 alpha-ketoglutarate transporter; Provisional; Region: PRK10406 907238000918 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 907238000919 putative substrate translocation pore; other site 907238000920 DNA segregation ATPase FtsK/SpoIIIE and related proteins [Cell division and chromosome partitioning]; Region: FtsK; COG1674 907238000921 TspO/MBR family; Region: TspO_MBR; cl01379 907238000922 FtsK/SpoIIIE family; Region: FtsK_SpoIIIE; pfam01580 907238000923 Ftsk gamma domain; Region: Ftsk_gamma; pfam09397 907238000924 Inactivated superfamily I helicase [DNA replication, recombination, and repair]; Region: COG3893 907238000925 RecB family exonuclease [DNA replication, recombination, and repair]; Region: COG2887 907238000926 transketolase, bacterial and yeast; Region: tktlase_bact; TIGR00232 907238000927 Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the...; Region: TPP_TK; cd02012 907238000928 TPP-binding site [chemical binding]; other site 907238000929 dimer interface [polypeptide binding]; other site 907238000930 Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins; Region: TPP_PYR_DXS_TK_like; cd07033 907238000931 PYR/PP interface [polypeptide binding]; other site 907238000932 dimer interface [polypeptide binding]; other site 907238000933 TPP binding site [chemical binding]; other site 907238000934 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 907238000935 FAD synthetase, N-terminal domain of the bifunctional enzyme; Region: FAD_synthetase_N; cd02064 907238000936 riboflavin kinase/FMN adenylyltransferase; Region: ribF; TIGR00083 907238000937 active site 907238000938 Riboflavin kinase; Region: Flavokinase; smart00904 907238000939 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 907238000940 hemolysin TlyA family protein; Region: tly; TIGR00478 907238000941 RNA binding surface [nucleotide binding]; other site 907238000942 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238000943 S-adenosylmethionine binding site [chemical binding]; other site 907238000944 aspartate carbamoyltransferase catalytic subunit; Provisional; Region: pyrB; PRK00856 907238000945 Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain; Region: OTCace_N; pfam02729 907238000946 Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain; Region: OTCace; pfam00185 907238000947 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238000948 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 907238000949 ABC transporter transmembrane region; Region: ABC_membrane; pfam00664 907238000950 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238000951 Walker A/P-loop; other site 907238000952 ATP binding site [chemical binding]; other site 907238000953 Q-loop/lid; other site 907238000954 ABC transporter signature motif; other site 907238000955 Walker B; other site 907238000956 D-loop; other site 907238000957 H-loop/switch region; other site 907238000958 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907238000959 Predicted endonuclease distantly related to archaeal Holliday junction resolvase and Mrr-like restriction enzymes [Defense mechanisms]; Region: COG1787 907238000960 Restriction endonuclease; Region: Mrr_cat; pfam04471 907238000961 Predicted ATPases [General function prediction only]; Region: COG1106 907238000962 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238000963 Walker A/P-loop; other site 907238000964 ATP binding site [chemical binding]; other site 907238000965 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238000966 Walker B; other site 907238000967 D-loop; other site 907238000968 H-loop/switch region; other site 907238000969 High-affinity nickel permease [Inorganic ion transport and metabolism]; Region: HoxN; COG3376 907238000970 M14 family of metallocarboxypeptidases and related proteins; Region: Peptidase_M14_like; cd00596 907238000971 active site 907238000972 Zn binding site [ion binding]; other site 907238000973 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 907238000974 metal-binding site [ion binding] 907238000975 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 907238000976 metal-binding site [ion binding] 907238000977 copper-(or silver)-translocating P-type ATPase; Region: ATPase-IB1_Cu; TIGR01511 907238000978 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 907238000979 Soluble P-type ATPase [General function prediction only]; Region: COG4087 907238000980 Phosphatidylserine synthase [Lipid metabolism]; Region: PssA; COG1183 907238000981 CDP-alcohol phosphatidyltransferase; Region: CDP-OH_P_transf; pfam01066 907238000982 ATP-dependent metalloprotease FtsH; Region: FtsH_fam; TIGR01241 907238000983 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238000984 Walker A motif; other site 907238000985 ATP binding site [chemical binding]; other site 907238000986 Walker B motif; other site 907238000987 arginine finger; other site 907238000988 Peptidase family M41; Region: Peptidase_M41; pfam01434 907238000989 ribosomal protein L11 methyltransferase; Region: prmA; TIGR00406 907238000990 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238000991 S-adenosylmethionine binding site [chemical binding]; other site 907238000992 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907238000993 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238000994 active site 907238000995 phosphorylation site [posttranslational modification] 907238000996 intermolecular recognition site; other site 907238000997 dimerization interface [polypeptide binding]; other site 907238000998 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238000999 rRNA small subunit methyltransferase G; Region: GidB; pfam02527 907238001000 16S rRNA (guanine(527)-N(7))-methyltransferase GidB; Region: gidB; TIGR00138 907238001001 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional; Region: queA; PRK00147 907238001002 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Region: queA; TIGR00113 907238001003 Sec-independent protein secretion pathway component TatC [Intracellular trafficking and secretion]; Region: TatC; COG0805 907238001004 sec-independent translocase; Provisional; Region: PRK04098 907238001005 Holliday junction DNA helicase RuvB; Reviewed; Region: ruvB; PRK00080 907238001006 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238001007 Walker A motif; other site 907238001008 ATP binding site [chemical binding]; other site 907238001009 Walker B motif; other site 907238001010 arginine finger; other site 907238001011 Holliday junction DNA helicase ruvB C-terminus; Region: RuvB_C; pfam05491 907238001012 Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a...; Region: KPHMT-like; cd06557 907238001013 oligomerization interface [polypeptide binding]; other site 907238001014 active site 907238001015 metal binding site [ion binding]; metal-binding site 907238001016 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001017 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001018 potential frameshift: common BLAST hit: gi|210134588|ref|YP_002301027.1| metalloendopeptidase related membrane protein 907238001019 septum formation inhibitor; Reviewed; Region: minC; PRK00556 907238001020 Septum formation inhibitor MinC, C-terminal domain; Region: MinC_C; pfam03775 907238001021 UDP-3-0-acyl N-acetylglucosamine deacetylase; Region: lpxC; TIGR00325 907238001022 UDP-3-O-acyl N-acetylglycosamine deacetylase; Region: LpxC; pfam03331 907238001023 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214 907238001024 homoserine kinase; Region: thrB; TIGR00191 907238001025 GHMP kinases N terminal domain; Region: GHMP_kinases_N; pfam00288 907238001026 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]; Region: COG2740 907238001027 putative RNA binding cleft [nucleotide binding]; other site 907238001028 translation initiation factor IF-2; Region: IF-2; TIGR00487 907238001029 Translation initiation factor IF-2, N-terminal region; Region: IF2_N; pfam04760 907238001030 Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family; Region: IF2_eIF5B; cd01887 907238001031 G1 box; other site 907238001032 putative GEF interaction site [polypeptide binding]; other site 907238001033 GTP/Mg2+ binding site [chemical binding]; other site 907238001034 Switch I region; other site 907238001035 G2 box; other site 907238001036 G3 box; other site 907238001037 Switch II region; other site 907238001038 G4 box; other site 907238001039 G5 box; other site 907238001040 This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell; Region: IF2_mtIF2_II; cd03702 907238001041 Translation-initiation factor 2; Region: IF-2; pfam11987 907238001042 mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor...; Region: mtIF2_IVc; cd03692 907238001043 Ribosome-binding factor A; Region: RBFA; cl00542 907238001044 Uncharacterized BCR, YhbC family COG0779; Region: DUF150; pfam02576 907238001045 Sm and related proteins; Region: Sm_like; cl00259 907238001046 Bacillus subtilis YxlS-like, C-terminal domain; Region: YlxS_C; cd01734 907238001047 putative oligomer interface [polypeptide binding]; other site 907238001048 putative RNA binding site [nucleotide binding]; other site 907238001049 acetyl-CoA synthetase; Provisional; Region: PRK00174 907238001050 Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme); Region: ACS; cd05966 907238001051 active site 907238001052 CoA binding site [chemical binding]; other site 907238001053 acyl-activating enzyme (AAE) consensus motif; other site 907238001054 AMP binding site [chemical binding]; other site 907238001055 acetate binding site [chemical binding]; other site 907238001056 Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain; Region: MPP_YkuE_C; cd07385 907238001057 putative active site [active] 907238001058 putative metal binding site [ion binding]; other site 907238001059 Calcineurin-like phosphoesterase; Region: Metallophos; pfam00149 907238001060 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 907238001061 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238001062 active site 907238001063 intermolecular recognition site; other site 907238001064 dimerization interface [polypeptide binding]; other site 907238001065 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 907238001066 DNA binding site [nucleotide binding] 907238001067 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]; Region: COG2404 907238001068 flagellar biosynthesis protein FlhA; Region: FlhA; TIGR01398 907238001069 FHIPEP family; Region: FHIPEP; pfam00771 907238001070 Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome; Region: Ribosomal_S15p_S13e; cd00353 907238001071 16S/18S rRNA binding site [nucleotide binding]; other site 907238001072 S13e-L30e interaction site [polypeptide binding]; other site 907238001073 25S rRNA binding site [nucleotide binding]; other site 907238001074 Lipid A core - O-antigen ligase and related enzymes [Cell envelope biogenesis, outer membrane]; Region: RfaL; COG3307 907238001075 O-Antigen ligase; Region: Wzy_C; pfam04932 907238001076 Dehydroquinase class II; Region: DHquinase_II; pfam01220 907238001077 Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway...; Region: DHQase_II; cd00466 907238001078 trimer interface [polypeptide binding]; other site 907238001079 active site 907238001080 dimer interface [polypeptide binding]; other site 907238001081 Creatinase/Prolidase N-terminal domain; Region: Creatinase_N; pfam01321 907238001082 Xaa-Pro aminopeptidase [Amino acid transport and metabolism]; Region: PepP; COG0006 907238001083 Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline; Region: APP-like; cd01092 907238001084 active site 907238001085 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after...; Region: HPPK; cd00483 907238001086 catalytic center binding site [active] 907238001087 ATP binding site [chemical binding]; other site 907238001088 flagellar biosynthesis regulator FlhF; Validated; Region: flhF; PRK05703 907238001089 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 907238001090 Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]; Region: flhG; COG0455 907238001091 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 907238001092 FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by...; Region: FleN-like; cd02038 907238001093 flagellar biosynthesis sigma factor; Validated; Region: fliA; PRK06986 907238001094 Sigma-70 region 2; Region: Sigma70_r2; pfam04542 907238001095 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or...; Region: Sigma70_r4; cd06171 907238001096 DNA binding residues [nucleotide binding] 907238001097 flagellar motor switch protein FliM; Validated; Region: fliM; PRK06666 907238001098 Surface presentation of antigens (SPOA); Region: SpoA; pfam01052 907238001099 flagellar motor switch protein FliY; Validated; Region: PRK08432 907238001100 flagellar motor switch protein FliN; Region: fliN; TIGR02480 907238001101 Domain of unknown function (DUF386); Region: DUF386; cl01047 907238001102 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4731 907238001103 Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Region: Fur_like; cd07153 907238001104 metal binding site 2 [ion binding]; metal-binding site 907238001105 putative DNA binding helix; other site 907238001106 metal binding site 1 [ion binding]; metal-binding site 907238001107 dimer interface [polypeptide binding]; other site 907238001108 structural Zn2+ binding site [ion binding]; other site 907238001109 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]; Region: MGS1; COG2256 907238001110 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238001111 Walker A motif; other site 907238001112 ATP binding site [chemical binding]; other site 907238001113 Walker B motif; other site 907238001114 arginine finger; other site 907238001115 MgsA AAA+ ATPase C terminal; Region: MgsA_C; pfam12002 907238001116 Helix-Turn-Helix DNA binding domain of the HspR transcription regulator; Region: HTH_HspR; cd04766 907238001117 MerR HTH family regulatory protein; Region: MerR_1; pfam13411 907238001118 DNA binding residues [nucleotide binding] 907238001119 putative dimer interface [polypeptide binding]; other site 907238001120 chaperone protein DnaJ; Provisional; Region: PRK14299 907238001121 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 907238001122 HSP70 interaction site [polypeptide binding]; other site 907238001123 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 907238001124 substrate binding site [polypeptide binding]; other site 907238001125 dimer interface [polypeptide binding]; other site 907238001126 5'-3' exonuclease; Provisional; Region: PRK14976 907238001127 PIN (PilT N terminus) domain: Superfamily; Region: PIN_SF; cl14812 907238001128 putative active site [active] 907238001129 Helix-hairpin-helix class 2 (Pol1 family) motifs; Region: HhH2; smart00279 907238001130 DNA binding site [nucleotide binding] 907238001131 metal binding site [ion binding]; metal-binding site 907238001132 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907238001133 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238001134 active site 907238001135 dimerization interface [polypeptide binding]; other site 907238001136 bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional; Region: ispDF; PRK09382 907238001137 CDP-ME synthetase is involved in mevalonate-independent isoprenoid production; Region: CDP-ME_synthetase; cd02516 907238001138 substrate binding site; other site 907238001139 dimer interface; other site 907238001140 MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis; Region: MECDP_synthase; cd00554 907238001141 homotrimer interaction site [polypeptide binding]; other site 907238001142 zinc binding site [ion binding]; other site 907238001143 CDP-binding sites; other site 907238001144 periplasmic serine protease, Do/DeqQ family; Region: degP_htrA_DO; TIGR02037 907238001145 Trypsin-like peptidase domain; Region: Trypsin_2; pfam13365 907238001146 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 907238001147 protein binding site [polypeptide binding]; other site 907238001148 PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind...; Region: PDZ_serine_protease; cd00987 907238001149 protein binding site [polypeptide binding]; other site 907238001150 S-methylmethionine transporter; Provisional; Region: PRK11387 907238001151 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase; Region: pgsA; TIGR00560 907238001152 7-alpha-hydroxysteroid dehydrogenase; Provisional; Region: PRK08416 907238001153 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs; Region: ChcA_like_SDR_c; cd05359 907238001154 putative NAD(P) binding site [chemical binding]; other site 907238001155 active site 907238001156 dihydrodipicolinate synthase; Region: dapA; TIGR00674 907238001157 Dihydrodipicolinate synthase (DHDPS); Region: DHDPS; cd00950 907238001158 dimer interface [polypeptide binding]; other site 907238001159 active site 907238001160 catalytic residue [active] 907238001161 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 907238001162 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 907238001163 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 907238001164 dihydroorotate dehydrogenase, subfamily 2; Region: pyrD_sub2; TIGR01036 907238001165 Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires...; Region: DHOD_2_like; cd04738 907238001166 quinone interaction residues [chemical binding]; other site 907238001167 active site 907238001168 catalytic residues [active] 907238001169 FMN binding site [chemical binding]; other site 907238001170 substrate binding site [chemical binding]; other site 907238001171 Polyphosphate kinase [Inorganic ion transport and metabolism]; Region: Ppk; COG0855 907238001172 Polyphosphate kinase N-terminal domain; Region: PP_kinase_N; pfam13089 907238001173 Polyphosphate kinase middle domain; Region: PP_kinase; pfam02503 907238001174 Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C1_like; cd09165 907238001175 putative domain interface [polypeptide binding]; other site 907238001176 putative active site [active] 907238001177 catalytic site [active] 907238001178 Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins; Region: PLDc_PaPPK1_C2_like; cd09168 907238001179 putative active site [active] 907238001180 putative domain interface [polypeptide binding]; other site 907238001181 catalytic site [active] 907238001182 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238001183 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907238001184 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 907238001185 Methyltransferase domain; Region: Methyltransf_26; pfam13659 907238001186 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 907238001187 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 907238001188 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238001189 ATP binding site [chemical binding]; other site 907238001190 putative Mg++ binding site [ion binding]; other site 907238001191 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2604 907238001192 N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins; Region: terB_like_DjlA; cd07316 907238001193 putative metal binding site [ion binding]; other site 907238001194 CoB--CoM heterodisulfide reductase, subunit B; Region: CoB_CoM_SS_B; TIGR03288 907238001195 oligoendopeptidase, pepF/M3 family; Region: M3_fam_3; TIGR02290 907238001196 Peptidase family M3B Oligopeptidase F (PepF); Region: M3B_PepF_5; cd09610 907238001197 active site 907238001198 Zn binding site [ion binding]; other site 907238001199 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 907238001200 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 907238001201 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001202 ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: ModA; COG0725 907238001203 Bacterial extracellular solute-binding protein; Region: SBP_bac_1; cl17199 907238001204 potential frameshift: common BLAST hit: gi|308182621|ref|YP_003926748.1| molybdenum ABC transporter ModB 907238001205 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238001206 putative bacteriocin export ABC transporter, lactococcin 972 group; Region: L_ocin_972_ABC; TIGR03608 907238001207 Walker A/P-loop; other site 907238001208 ATP binding site [chemical binding]; other site 907238001209 Q-loop/lid; other site 907238001210 ABC transporter signature motif; other site 907238001211 Walker B; other site 907238001212 D-loop; other site 907238001213 H-loop/switch region; other site 907238001214 glutamyl-tRNA synthetase; Reviewed; Region: gltX; PRK01406 907238001215 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 907238001216 active site 907238001217 HIGH motif; other site 907238001218 nucleotide binding site [chemical binding]; other site 907238001219 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 907238001220 active site 907238001221 KMSKS motif; other site 907238001222 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001223 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 907238001224 Methyltransferase domain; Region: Methyltransf_26; pfam13659 907238001225 TaqI-like C-terminal specificity domain; Region: TaqI_C; pfam12950 907238001226 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907238001227 ADP-heptose:LPS heptosyl transferase I; Provisional; Region: PRK10964; cl15782 907238001228 Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]; Region: TypA; COG1217 907238001229 Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases; Region: TypA_BipA; cd01891 907238001230 G1 box; other site 907238001231 putative GEF interaction site [polypeptide binding]; other site 907238001232 GTP/Mg2+ binding site [chemical binding]; other site 907238001233 Switch I region; other site 907238001234 G2 box; other site 907238001235 G3 box; other site 907238001236 Switch II region; other site 907238001237 G4 box; other site 907238001238 G5 box; other site 907238001239 BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a...; Region: BipA_TypA_II; cd03691 907238001240 BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly...; Region: BipA_TypA_C; cd03710 907238001241 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dam; COG0338 907238001242 Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins; Region: GIY-YIG_EndoII_Hpy188I_like; cd10436 907238001243 GIY-YIG motif/motif A; other site 907238001244 DNA binding site [nucleotide binding] 907238001245 active site 907238001246 catalytic site [active] 907238001247 metal binding site [ion binding]; metal-binding site 907238001248 Site-specific DNA methylase [DNA replication, recombination, and repair]; Region: Dcm; COG0270 907238001249 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 907238001250 cofactor binding site; other site 907238001251 DNA binding site [nucleotide binding] 907238001252 substrate interaction site [chemical binding]; other site 907238001253 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 907238001254 Catalase-like heme-binding proteins similar to the uncharacterized srpA; Region: srpA_like; cd08153 907238001255 putative heme binding pocket [chemical binding]; other site 907238001256 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238001257 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238001258 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238001259 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238001260 Uncharacterized conserved protein [Function unknown]; Region: COG1432 907238001261 LabA_like proteins; Region: LabA_like; cd06167 907238001262 putative metal binding site [ion binding]; other site 907238001263 Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD...; Region: RuvC_resolvase; cd00529 907238001264 active site 907238001265 putative DNA-binding cleft [nucleotide binding]; other site 907238001266 dimer interface [polypeptide binding]; other site 907238001267 Outer membrane receptor proteins, mostly Fe transport [Inorganic ion transport and metabolism]; Region: CirA; COG1629 907238001268 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 907238001269 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 907238001270 Catalase [Inorganic ion transport and metabolism]; Region: KatE; COG0753 907238001271 Clade 3 of the heme-binding enzyme catalase; Region: catalase_clade_3; cd08156 907238001272 tetramer interface [polypeptide binding]; other site 907238001273 heme binding pocket [chemical binding]; other site 907238001274 NADPH binding site [chemical binding]; other site 907238001275 alkylphosphonate utilization operon protein PhnA; Region: phnA; TIGR00686 907238001276 PhnA Zinc-Ribbon; Region: PhnA_Zn_Ribbon; pfam08274 907238001277 PhnA protein; Region: PhnA; pfam03831 907238001278 CDP-diacylglycerol pyrophosphatase; Region: CDH; cl00934 907238001279 flagellar hook protein FlgE; Validated; Region: flgE; PRK08425 907238001280 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 907238001281 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907238001282 Flagellar basal body protein FlaE; Region: FlaE; pfam07559 907238001283 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907238001284 hydrogenase nickel incorporation protein; Provisional; Region: hypA; PRK00564 907238001285 Hydrogenase expression/synthesis hypA family; Region: HypA; pfam01155 907238001286 ipid-A-disaccharide synthase; Provisional; Region: PRK14089 907238001287 lipid-A-disaccharide synthase; Region: lpxB; TIGR00215 907238001288 transcription elongation factor GreA; Reviewed; Region: greA; PRK00226 907238001289 Transcription elongation factor, N-terminal; Region: GreA_GreB_N; pfam03449 907238001290 Transcription elongation factor, GreA/GreB, C-term; Region: GreA_GreB; pfam01272 907238001291 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 907238001292 trimer interface [polypeptide binding]; other site 907238001293 active site 907238001294 PQQ-like domain; Region: PQQ_2; pfam13360 907238001295 pantothenate kinase; Reviewed; Region: PRK13333 907238001296 Uncharacterized conserved protein [Function unknown]; Region: COG2836 907238001297 D,D-heptose 1,7-bisphosphate phosphatase; Region: GmhB_yaeD; TIGR00213 907238001298 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 907238001299 active site 907238001300 motif I; other site 907238001301 motif II; other site 907238001302 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 907238001303 ADP-L-glycero-D-manno-heptose-6-epimerase; Region: heptose_epim; TIGR02197 907238001304 NAD(P) binding site [chemical binding]; other site 907238001305 active site 907238001306 ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaE; COG2870 907238001307 RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer...; Region: RfaE_like; cd01172 907238001308 putative ribose interaction site [chemical binding]; other site 907238001309 putative ADP binding site [chemical binding]; other site 907238001310 rfaE bifunctional protein, domain II; Region: rfaE_dom_II; TIGR02199 907238001311 active site 907238001312 nucleotide binding site [chemical binding]; other site 907238001313 HIGH motif; other site 907238001314 KMSKS motif; other site 907238001315 Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of...; Region: SIS_GmhA; cd05006 907238001316 dimer interface [polypeptide binding]; other site 907238001317 active site 907238001318 guanosine 5'-monophosphate oxidoreductase; Provisional; Region: PRK05458 907238001319 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 907238001320 active site 907238001321 ABC transporter ATP-binding protein; Provisional; Region: PRK15064 907238001322 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238001323 Walker A/P-loop; other site 907238001324 ATP binding site [chemical binding]; other site 907238001325 Q-loop/lid; other site 907238001326 ABC transporter signature motif; other site 907238001327 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 907238001328 Walker B; other site 907238001329 D-loop; other site 907238001330 H-loop/switch region; other site 907238001331 ABC transporter; Region: ABC_tran_2; pfam12848 907238001332 ATP-binding cassette domain of elongation factor 3, subfamily F; Region: ABCF_EF-3; cd03221 907238001333 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2958 907238001334 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_2; cd03392 907238001335 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 907238001336 active site 907238001337 type I restriction system adenine methylase (hsdM); Region: hsdM; TIGR00497 907238001338 HsdM N-terminal domain; Region: HsdM_N; pfam12161 907238001339 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238001340 S-adenosylmethionine binding site [chemical binding]; other site 907238001341 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238001342 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907238001343 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238001344 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases [Defense mechanisms]; Region: COG0610 907238001345 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 907238001346 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238001347 ATP binding site [chemical binding]; other site 907238001348 putative Mg++ binding site [ion binding]; other site 907238001349 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine...; Region: THZ_kinase; cd01170 907238001350 substrate binding site [chemical binding]; other site 907238001351 multimerization interface [polypeptide binding]; other site 907238001352 ATP binding site [chemical binding]; other site 907238001353 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of...; Region: HMPP_kinase; cd01169 907238001354 dimer interface [polypeptide binding]; other site 907238001355 substrate binding site [chemical binding]; other site 907238001356 ATP binding site [chemical binding]; other site 907238001357 Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5-; Region: TMP_TenI; cd00564 907238001358 thiamine phosphate binding site [chemical binding]; other site 907238001359 active site 907238001360 pyrophosphate binding site [ion binding]; other site 907238001361 phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase; Region: coaBC_dfp; TIGR00521 907238001362 Flavoprotein; Region: Flavoprotein; pfam02441 907238001363 DNA / pantothenate metabolism flavoprotein; Region: DFP; pfam04127 907238001364 UDP-N-acetylglucosamine 4,6-dehydratase; Region: PseB; TIGR03589 907238001365 UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs; Region: UDP_invert_4-6DH_SDR_e; cd05237 907238001366 NAD(P) binding site [chemical binding]; other site 907238001367 homodimer interface [polypeptide binding]; other site 907238001368 substrate binding site [chemical binding]; other site 907238001369 active site 907238001370 Long-chain fatty acid transport protein [Lipid metabolism]; Region: FadL; COG2067 907238001371 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 907238001372 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3018 907238001373 Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and...; Region: HU_IHF; cd00591 907238001374 IHF dimer interface [polypeptide binding]; other site 907238001375 IHF - DNA interface [nucleotide binding]; other site 907238001376 GTP-binding protein Der; Reviewed; Region: PRK00093 907238001377 EngA1 GTPase contains the first domain of EngA; Region: EngA1; cd01894 907238001378 G1 box; other site 907238001379 GTP/Mg2+ binding site [chemical binding]; other site 907238001380 Switch I region; other site 907238001381 G2 box; other site 907238001382 Switch II region; other site 907238001383 G3 box; other site 907238001384 G4 box; other site 907238001385 G5 box; other site 907238001386 EngA2 GTPase contains the second domain of EngA; Region: EngA2; cd01895 907238001387 G1 box; other site 907238001388 GTP/Mg2+ binding site [chemical binding]; other site 907238001389 Switch I region; other site 907238001390 G2 box; other site 907238001391 G3 box; other site 907238001392 Switch II region; other site 907238001393 G4 box; other site 907238001394 G5 box; other site 907238001395 spermidine synthase; Provisional; Region: speE; PRK00536 907238001396 spermidine synthase; Provisional; Region: PRK00811 907238001397 Dephospho-CoA kinase [Coenzyme metabolism]; Region: CoaE; COG0237 907238001398 Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis; Region: DPCK; cd02022 907238001399 CoA-binding site [chemical binding]; other site 907238001400 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit; Region: gatA; TIGR00132 907238001401 indole acetimide hydrolase; Validated; Region: PRK07488 907238001402 inosine 5'-monophosphate dehydrogenase; Reviewed; Region: PRK05567 907238001403 TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate...; Region: TIM_phosphate_binding; cl17186 907238001404 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a...; Region: CBS_pair_IMPDH; cd04601 907238001405 IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of...; Region: IMPDH; cd00381 907238001406 active site 907238001407 F0F1-type ATP synthase, subunit a [Energy production and conversion]; Region: AtpB; COG0356 907238001408 F0F1 ATP synthase subunit A; Validated; Region: PRK05815 907238001409 RNA recognition motif in Helicobacter pylori HP0827 protein and similar proteins; Region: RRM_HP0827_like; cd12399 907238001410 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907238001411 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 907238001412 thioredoxin-disulfide reductase; Region: TRX_reduct; TIGR01292 907238001413 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 907238001414 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 907238001415 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 907238001416 Thioredoxin-like; Region: Thioredoxin_8; pfam13905 907238001417 catalytic residues [active] 907238001418 Predicted endonuclease distantly related to archaeal Holliday junction resolvase [DNA replication, recombination, and repair]; Region: COG0792 907238001419 homoserine dehydrogenase; Provisional; Region: PRK06349 907238001420 Homoserine dehydrogenase; Region: Homoserine_dh; pfam00742 907238001421 ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains; Region: ACT_HSDH-Hom; cd04881 907238001422 excinuclease ABC, C subunit; Region: uvrC; TIGR00194 907238001423 Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins; Region: GIY-YIG_UvrC_Cho; cd10434 907238001424 GIY-YIG motif/motif A; other site 907238001425 active site 907238001426 catalytic site [active] 907238001427 putative DNA binding site [nucleotide binding]; other site 907238001428 metal binding site [ion binding]; metal-binding site 907238001429 UvrB/uvrC motif; Region: UVR; pfam02151 907238001430 UvrC Helix-hairpin-helix N-terminal; Region: UvrC_HhH_N; pfam08459 907238001431 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907238001432 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238001433 Walker A/P-loop; other site 907238001434 ATP binding site [chemical binding]; other site 907238001435 Q-loop/lid; other site 907238001436 ABC transporter signature motif; other site 907238001437 Walker B; other site 907238001438 D-loop; other site 907238001439 H-loop/switch region; other site 907238001440 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238001441 dimer interface [polypeptide binding]; other site 907238001442 conserved gate region; other site 907238001443 ABC-ATPase subunit interface; other site 907238001444 Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]; Region: OpuBC; COG1732 907238001445 flagellar motor protein MotB; Reviewed; Region: motB; PRK08457 907238001446 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 907238001447 ligand binding site [chemical binding]; other site 907238001448 Flagellar motor component [Cell motility and secretion]; Region: MotA; COG1291 907238001449 flagellar motor protein MotA; Validated; Region: PRK08456 907238001450 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 2 [Coenzyme metabolism]; Region: ThiF; COG0476 907238001451 ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD...; Region: ThiF_MoeB_HesA_family; cd00757 907238001452 ATP binding site [chemical binding]; other site 907238001453 substrate interface [chemical binding]; other site 907238001454 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 907238001455 Uncharacterized conserved protein [Function unknown]; Region: COG1565 907238001456 RNA methyltransferase, RsmD family; Region: TIGR00095 907238001457 N6-adenine-specific methylase [DNA replication, recombination, and repair]; Region: COG0742 907238001458 flagellar basal body-associated protein FliL; Reviewed; Region: fliL; PRK08455 907238001459 holo-[acyl-carrier-protein] synthase; Region: acpS; TIGR00516 907238001460 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 907238001461 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 907238001462 N-terminal plug; other site 907238001463 ligand-binding site [chemical binding]; other site 907238001464 Predicted metal-dependent hydrolase [General function prediction only]; Region: COG1451 907238001465 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907238001466 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional; Region: PRK09314 907238001467 3,4-dihydroxy-2-butanone 4-phosphate synthase; Region: ribB; TIGR00506 907238001468 GTP cyclohydrolase II [Coenzyme metabolism]; Region: RibA; COG0807 907238001469 Domain of unknown function (DUF3943); Region: DUF3943; pfam13084 907238001470 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the...; Region: GTP_cyclohydro2; cd00641 907238001471 dimerization interface [polypeptide binding]; other site 907238001472 active site 907238001473 Ubiquitin domain of MoaD-like proteins; Region: MoaD; cd00754 907238001474 MoaE interaction surface [polypeptide binding]; other site 907238001475 MoeB interaction surface [polypeptide binding]; other site 907238001476 thiocarboxylated glycine; other site 907238001477 MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and...; Region: MoaE; cd00756 907238001478 MoaE homodimer interface [polypeptide binding]; other site 907238001479 MoaD interaction [polypeptide binding]; other site 907238001480 active site residues [active] 907238001481 MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea; Region: MogA_MoaB; cd00886 907238001482 MPT binding site; other site 907238001483 trimer interface [polypeptide binding]; other site 907238001484 MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine...; Region: MoaC_PE; cd01420 907238001485 trimer interface [polypeptide binding]; other site 907238001486 dimer interface [polypeptide binding]; other site 907238001487 putative active site [active] 907238001488 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907238001489 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001490 trigger factor; Provisional; Region: tig; PRK01490 907238001491 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 907238001492 Bacterial trigger factor protein (TF) C-terminus; Region: Trigger_C; pfam05698 907238001493 Protease subunit of ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]; Region: ClpP; COG0740 907238001494 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease; Region: S14_ClpP_2; cd07017 907238001495 oligomer interface [polypeptide binding]; other site 907238001496 active site residues [active] 907238001497 Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II)...; Region: Pep_deformylase; cd00487 907238001498 active site 907238001499 catalytic residues [active] 907238001500 metal binding site [ion binding]; metal-binding site 907238001501 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]; Region: COG0606 907238001502 Subunit ChlI of Mg-chelatase; Region: ChlI; pfam13541 907238001503 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 907238001504 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase_2; pfam13335 907238001505 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cl00207 907238001506 metal-binding site [ion binding] 907238001507 heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase; Region: ATPase-IB2_Cd; TIGR01512 907238001508 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 907238001509 Soluble P-type ATPase [General function prediction only]; Region: COG4087 907238001510 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238001511 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907238001512 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238001513 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238001514 ABC-type transport system, involved in lipoprotein release, permease component [Cell envelope biogenesis, outer membrane]; Region: LolE; COG4591 907238001515 FtsX-like permease family; Region: FtsX; pfam02687 907238001516 preprotein translocase subunit SecA; Reviewed; Region: PRK12904 907238001517 SecA preprotein cross-linking domain; Region: SecA_PP_bind; smart00958 907238001518 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 907238001519 nucleotide binding region [chemical binding]; other site 907238001520 ATP-binding site [chemical binding]; other site 907238001521 SEC-C motif; Region: SEC-C; pfam02810 907238001522 lipoprotein chaperone; Reviewed; Region: lolA; PRK00031 907238001523 Outer membrane lipoprotein carrier protein LolA; Region: LolA; pfam03548 907238001524 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238001525 FOG: Transposase [DNA replication, recombination, and repair]; Region: COG5659 907238001526 aconitate hydratase 2; Region: acnB; TIGR00117 907238001527 Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in...; Region: AcnB_Swivel; cd01576 907238001528 substrate binding site [chemical binding]; other site 907238001529 Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle; Region: AcnB; cd01581 907238001530 substrate binding site [chemical binding]; other site 907238001531 ligand binding site [chemical binding]; other site 907238001532 Predicted periplasmic solute-binding protein [General function prediction only]; Region: COG1427 907238001533 UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and...; Region: AAK_UMPK-PyrH-Ec; cd04254 907238001534 putative nucleotide binding site [chemical binding]; other site 907238001535 uridine monophosphate binding site [chemical binding]; other site 907238001536 homohexameric interface [polypeptide binding]; other site 907238001537 DNA-directed RNA polymerase, subunit K/omega [Transcription]; Region: RpoZ; COG1758 907238001538 (p)ppGpp synthetase, RelA/SpoT family; Region: spoT_relA; TIGR00691 907238001539 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 907238001540 Zn2+ binding site [ion binding]; other site 907238001541 Mg2+ binding site [ion binding]; other site 907238001542 Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases; Region: NT_Rel-Spo_like; cd05399 907238001543 synthetase active site [active] 907238001544 NTP binding site [chemical binding]; other site 907238001545 metal binding site [ion binding]; metal-binding site 907238001546 TGS_RelA_SpoT: The RelA (SpoT) protein, also referred to as ppGpp hydrolase/synthetase, is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. RelA contains a TGS domain, named after...; Region: TGS_RelA_SpoT; cd01668 907238001547 tyrosyl-tRNA synthetase; Validated; Region: PRK05912 907238001548 catalytic core domain of tyrosinyl-tRNA synthetase; Region: TyrRS_core; cd00805 907238001549 active site 907238001550 HIGH motif; other site 907238001551 dimer interface [polypeptide binding]; other site 907238001552 KMSKS motif; other site 907238001553 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 907238001554 RNA binding surface [nucleotide binding]; other site 907238001555 Nitronate monooxygenase; Region: NMO; pfam03060 907238001556 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase...; Region: NPD_like; cd04730 907238001557 FMN binding site [chemical binding]; other site 907238001558 substrate binding site [chemical binding]; other site 907238001559 putative catalytic residue [active] 907238001560 N-acetylmuramoyl-L-alanine amidase [Cell envelope biogenesis, outer membrane]; Region: AmiC; COG0860 907238001561 N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino...; Region: MurNAc-LAA; cd02696 907238001562 active site 907238001563 metal binding site [ion binding]; metal-binding site 907238001564 flagellar biosynthetic protein FlhB; Region: flhB; TIGR00328 907238001565 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]; Region: COG2257 907238001566 Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]; Region: FlhB; COG1377 907238001567 molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed; Region: mobA; PRK00317 907238001568 MobA catalyzes the formation of molybdopterin guanine dinucleotide; Region: MobA; cd02503 907238001569 GTP binding site; other site 907238001570 molybdenum cofactor biosynthesis protein A; Reviewed; Region: moaA; PRK00164 907238001571 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238001572 FeS/SAM binding site; other site 907238001573 Molybdenum Cofactor Synthesis C; Region: Mob_synth_C; pfam06463 907238001574 Flagellin N-methylase; Region: FliB; pfam03692 907238001575 signal recognition particle-docking protein FtsY; Region: ftsY; TIGR00064 907238001576 The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion; Region: Fer4_NifH; cl17203 907238001577 5-formyltetrahydrofolate cyclo-ligase [Coenzyme metabolism]; Region: COG0212 907238001578 phosphodiesterase; Provisional; Region: PRK12704 907238001579 K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that...; Region: KH-I; cd00105 907238001580 nucleic acid binding region [nucleotide binding]; other site 907238001581 G-X-X-G motif; other site 907238001582 Metal dependent phosphohydrolases with conserved 'HD' motif; Region: HDc; cd00077 907238001583 Zn2+ binding site [ion binding]; other site 907238001584 Mg2+ binding site [ion binding]; other site 907238001585 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM; Region: MATE_NorM_like; cd13137 907238001586 putative efflux protein, MATE family; Region: matE; TIGR00797 907238001587 Predicted permease [General function prediction only]; Region: COG2056 907238001588 Na+-H+ antiporter family; Region: Na_H_antiport_2; pfam13726 907238001589 N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases); Region: CPA; cd07573 907238001590 N-carbamoylputrescine amidase; Region: agmatine_aguB; TIGR03381 907238001591 putative active site; other site 907238001592 catalytic triad [active] 907238001593 putative dimer interface [polypeptide binding]; other site 907238001594 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]; Region: COG1179 907238001595 Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like...; Region: YgdL_like; cd00755 907238001596 putative ATP binding site [chemical binding]; other site 907238001597 putative substrate interface [chemical binding]; other site 907238001598 flagellar biosynthetic protein FliS; Region: fliS; TIGR00208 907238001599 flagellar capping protein; Validated; Region: fliD; PRK08453 907238001600 Flagellar hook-associated protein 2 C-terminus; Region: FliD_N; pfam02465 907238001601 Flagellar hook-associated protein 2 C-terminus; Region: FliD_C; pfam07195 907238001602 flagellar protein FlaG; Provisional; Region: PRK08452 907238001603 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907238001604 Peptidase family M23; Region: Peptidase_M23; pfam01551 907238001605 putative protein insertion permease FtsX; Region: ftsX; TIGR00439 907238001606 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907238001607 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 907238001608 Walker A/P-loop; other site 907238001609 ATP binding site [chemical binding]; other site 907238001610 Q-loop/lid; other site 907238001611 ABC transporter signature motif; other site 907238001612 Walker B; other site 907238001613 D-loop; other site 907238001614 H-loop/switch region; other site 907238001615 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238001616 S-adenosylmethionine binding site [chemical binding]; other site 907238001617 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cl00065 907238001618 Fibronectin type 3 domain-containing protein [General function prediction only]; Region: COG3401 907238001619 Interdomain contacts; other site 907238001620 Cytokine receptor motif; other site 907238001621 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 907238001622 Interdomain contacts; other site 907238001623 Cytokine receptor motif; other site 907238001624 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all...; Region: FN3; cd00063 907238001625 Interdomain contacts; other site 907238001626 Cytokine receptor motif; other site 907238001627 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 907238001628 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 907238001629 active site 907238001630 rod shape-determining protein RodA; Region: rodA_shape; TIGR02210 907238001631 ribose-phosphate pyrophosphokinase; Provisional; Region: PRK01259 907238001632 N-terminal domain of ribose phosphate pyrophosphokinase; Region: Pribosyltran_N; pfam13793 907238001633 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907238001634 active site 907238001635 FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into...; Region: FHIT; cd01275 907238001636 nucleotide binding site/active site [active] 907238001637 HIT family signature motif; other site 907238001638 catalytic residue [active] 907238001639 UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]; Region: MurF; COG0770 907238001640 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907238001641 Alpha/beta hydrolase family; Region: Abhydrolase_6; pfam12697 907238001642 D-alanyl-alanine synthetase A; Reviewed; Region: ddl; PRK01966 907238001643 D-ala D-ala ligase N-terminus; Region: Dala_Dala_lig_N; pfam01820 907238001644 ATP-grasp domain; Region: ATP-grasp_4; cl17255 907238001645 Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism; Region: PgpA; cd06971 907238001646 tetramer interfaces [polypeptide binding]; other site 907238001647 binuclear metal-binding site [ion binding]; other site 907238001648 Serine-pyruvate aminotransferase/archaeal aspartate aminotransferase [Amino acid transport and metabolism]; Region: COG0075 907238001649 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 907238001650 catalytic residue [active] 907238001651 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG2236 907238001652 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907238001653 active site 907238001654 2-methylthioadenine synthetase [Translation, ribosomal structure and biogenesis]; Region: MiaB; COG0621 907238001655 Uncharacterized protein family UPF0004; Region: UPF0004; pfam00919 907238001656 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238001657 FeS/SAM binding site; other site 907238001658 Mitochondrial inner membrane protein; Region: Mitofilin; pfam09731 907238001659 potential frameshift: common BLAST hit: gi|254779290|ref|YP_003057395.1| putative LeoA protein 907238001660 potential frameshift: common BLAST hit: gi|254779290|ref|YP_003057395.1| putative LeoA protein 907238001661 Elongator protein 3, MiaB family, Radical SAM; Region: Elp3; smart00729 907238001662 tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]; Region: MesJ; COG0037 907238001663 N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control [Cell division and chromosome partitioning]. This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases...; Region: PP-ATPase; cd01992 907238001664 Ligand Binding Site [chemical binding]; other site 907238001665 tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]; Region: COG0042 907238001666 Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also...; Region: DUS_like_FMN; cd02801 907238001667 FMN binding site [chemical binding]; other site 907238001668 active site 907238001669 catalytic residues [active] 907238001670 substrate binding site [chemical binding]; other site 907238001671 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001672 anaerobic c4-dicarboxylate membrane transporter family protein; Region: Dcu; TIGR00770 907238001673 Anaerobic C4-dicarboxylate transporter [General function prediction only]; Region: DcuB; COG2704 907238001674 Type II (periplasmic) bacterial L-asparaginase; Region: L-asparaginase_II; cd08964 907238001675 active site 907238001676 homodimer interface [polypeptide binding]; other site 907238001677 homotetramer interface [polypeptide binding]; other site 907238001678 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001679 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 907238001680 Protein of unknown function (DUF1104); Region: DUF1104; pfam06518 907238001681 potential frameshift: common BLAST hit: gi|210134920|ref|YP_002301359.1| integral membrane protein 907238001682 DNA polymerase III subunits gamma and tau; Validated; Region: PRK08451 907238001683 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238001684 Walker A motif; other site 907238001685 ATP binding site [chemical binding]; other site 907238001686 Walker B motif; other site 907238001687 arginine finger; other site 907238001688 Uncharacterized P-loop hydrolase UPF0079; Region: UPF0079; cl00520 907238001689 ABC-type (unclassified) transport system, ATPase component [General function prediction only]; Region: YhbG; COG1137 907238001690 ATP-binding cassette component of YhbG transport system; Region: ABC_YhbG; cd03218 907238001691 Walker A/P-loop; other site 907238001692 ATP binding site [chemical binding]; other site 907238001693 Q-loop/lid; other site 907238001694 ABC transporter signature motif; other site 907238001695 Walker B; other site 907238001696 D-loop; other site 907238001697 H-loop/switch region; other site 907238001698 RNA polymerase factor sigma-54; Reviewed; Region: PRK05932 907238001699 Sigma-54 factor, Activator interacting domain (AID); Region: Sigma54_AID; pfam00309 907238001700 Sigma-54 factor, core binding domain; Region: Sigma54_CBD; pfam04963 907238001701 Sigma-54, DNA binding domain; Region: Sigma54_DBD; pfam04552 907238001702 Competence protein ComGF [Intracellular trafficking and secretion]; Region: ComGF; COG4940 907238001703 Predicted hydrolases of HD superfamily [General function prediction only]; Region: COG1896 907238001704 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001705 Uncharacterized conserved protein [Function unknown]; Region: COG1912 907238001706 16S rRNA (cytosine(1402)-N(4))-methyltransferase; Region: TIGR00006 907238001707 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]; Region: COG0275 907238001708 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001709 excinuclease ABC subunit A; Reviewed; Region: uvrA; PRK00349 907238001710 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 907238001711 ATP-binding cassette domain I of the excision repair protein UvrA; Region: ABC_UvrA_I; cd03270 907238001712 ATP-binding cassette domain II of the excision repair protein UvrA; Region: ABC_UvrA_II; cd03271 907238001713 Response regulator receiver domain; Region: Response_reg; pfam00072 907238001714 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238001715 active site 907238001716 phosphorylation site [posttranslational modification] 907238001717 intermolecular recognition site; other site 907238001718 dimerization interface [polypeptide binding]; other site 907238001719 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238001720 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 907238001721 Walker A motif; other site 907238001722 ATP binding site [chemical binding]; other site 907238001723 Walker B motif; other site 907238001724 arginine finger; other site 907238001725 DNA gyrase subunit A; Validated; Region: PRK05560 907238001726 DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes...; Region: TOP4c; cd00187 907238001727 CAP-like domain; other site 907238001728 active site 907238001729 primary dimer interface [polypeptide binding]; other site 907238001730 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907238001731 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907238001732 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907238001733 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907238001734 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907238001735 DNA gyrase C-terminal domain, beta-propeller; Region: DNA_gyraseA_C; pfam03989 907238001736 Diacylglycerol kinase [Cell envelope biogenesis, outer membrane]; Region: DgkA; COG0818 907238001737 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238001738 Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]; Region: AcxC; COG4647 907238001739 Acetone carboxylase gamma subunit; Region: Acetone_carb_G; pfam08882 907238001740 N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuB; COG0146 907238001741 Hydantoinase B/oxoprolinase; Region: Hydantoinase_B; pfam02538 907238001742 N-methylhydantoinase A/acetone carboxylase, beta subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]; Region: HyuA; COG0145 907238001743 Hydantoinase/oxoprolinase N-terminal region; Region: Hydant_A_N; pfam05378 907238001744 Hydantoinase/oxoprolinase; Region: Hydantoinase_A; pfam01968 907238001745 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3528 907238001746 Short chain fatty acid transporter; Region: SCFA_trans; pfam02667 907238001747 3-oxoacid CoA-transferase, B subunit; Region: pcaJ_scoB_fam; TIGR02428 907238001748 Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid metabolism]; Region: AtoD; COG1788 907238001749 putative acyltransferase; Provisional; Region: PRK05790 907238001750 Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and...; Region: thiolase; cd00751 907238001751 dimer interface [polypeptide binding]; other site 907238001752 active site 907238001753 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB [DNA replication, recombination, and repair]; Region: COG3298 907238001754 CfrBI restriction endonuclease; Region: RE_CfrBI; pfam09516 907238001755 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907238001756 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238001757 Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases; Region: DNA_polB_like1_exo; cd05782 907238001758 active site 907238001759 catalytic site [active] 907238001760 substrate binding site [chemical binding]; other site 907238001761 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; Region: DNA_pol_B_exo2; pfam10108 907238001762 Fe2+ transport system protein B [Inorganic ion transport and metabolism]; Region: FeoB; COG0370 907238001763 Ferrous iron transport protein B (FeoB) family; Region: FeoB; cd01879 907238001764 G1 box; other site 907238001765 GTP/Mg2+ binding site [chemical binding]; other site 907238001766 Switch I region; other site 907238001767 G2 box; other site 907238001768 G3 box; other site 907238001769 Switch II region; other site 907238001770 G4 box; other site 907238001771 G5 box; other site 907238001772 Nucleoside recognition; Region: Gate; pfam07670 907238001773 Ferrous iron transport protein B C terminus; Region: FeoB_C; pfam07664 907238001774 Nucleoside recognition; Region: Gate; pfam07670 907238001775 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 907238001776 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 907238001777 N-terminal plug; other site 907238001778 ligand-binding site [chemical binding]; other site 907238001779 flagellar biosynthesis protein FliP; Reviewed; Region: fliP; PRK05699 907238001780 bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional; Region: glmU; PRK14359 907238001781 N-terminal domain of bacterial GlmU; Region: GT2_GlmU_N_bac; cd02540 907238001782 Substrate binding site; other site 907238001783 Mg++ binding site; other site 907238001784 N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two...; Region: LbH_GlmU_C; cd03353 907238001785 active site 907238001786 substrate binding site [chemical binding]; other site 907238001787 CoA binding site [chemical binding]; other site 907238001788 ribonucleotide-diphosphate reductase subunit alpha; Validated; Region: PRK08447 907238001789 ATP cone domain; Region: ATP-cone; pfam03477 907238001790 Class I ribonucleotide reductase; Region: RNR_I; cd01679 907238001791 active site 907238001792 dimer interface [polypeptide binding]; other site 907238001793 catalytic residues [active] 907238001794 effector binding site; other site 907238001795 R2 peptide binding site; other site 907238001796 Predicted dehydrogenases and related proteins [General function prediction only]; Region: MviM; COG0673 907238001797 Oxidoreductase family, NAD-binding Rossmann fold; Region: GFO_IDH_MocA; pfam01408 907238001798 Oxidoreductase family, C-terminal alpha/beta domain; Region: GFO_IDH_MocA_C; pfam02894 907238001799 Sulfite exporter TauE/SafE; Region: TauE; pfam01925 907238001800 Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]; Region: Ada; COG0350 907238001801 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain; Region: Methyltransf_1N; pfam02870 907238001802 The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases...; Region: ATase; cd06445 907238001803 DNA binding site [nucleotide binding] 907238001804 active site 907238001805 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 907238001806 DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine recombinases that share the same fold in their catalytic domain containing six conserved active site...; Region: DNA_BRE_C; cl00213 907238001807 active site 907238001808 DNA binding site [nucleotide binding] 907238001809 Int/Topo IB signature motif; other site 907238001810 aspartate aminotransferase; Provisional; Region: PRK05764 907238001811 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 907238001812 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238001813 homodimer interface [polypeptide binding]; other site 907238001814 catalytic residue [active] 907238001815 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001816 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+; Region: SIR2; cl00195 907238001817 Predicted helicase [General function prediction only]; Region: COG4889 907238001818 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 907238001819 nucleotide binding region [chemical binding]; other site 907238001820 ATP-binding site [chemical binding]; other site 907238001821 Restriction endonuclease; Region: Mrr_cat; pfam04471 907238001822 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238001823 ATP binding site [chemical binding]; other site 907238001824 putative Mg++ binding site [ion binding]; other site 907238001825 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 907238001826 Cysteine-rich domain; Region: CCG; pfam02754 907238001827 Cysteine-rich domain; Region: CCG; pfam02754 907238001828 oxygen-independent coproporphyrinogen III oxidase; Region: hemN; TIGR00538 907238001829 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238001830 FeS/SAM binding site; other site 907238001831 HemN C-terminal domain; Region: HemN_C; pfam06969 907238001832 Protein of unknown function (DUF2603); Region: DUF2603; pfam10788 907238001833 Chorismate synthase [Amino acid transport and metabolism]; Region: AroC; COG0082 907238001834 Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway; Region: Chorismate_synthase; cd07304 907238001835 Tetramer interface [polypeptide binding]; other site 907238001836 active site 907238001837 FMN-binding site [chemical binding]; other site 907238001838 ribonuclease III; Reviewed; Region: rnc; PRK00102 907238001839 RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in...; Region: RIBOc; cd00593 907238001840 dimerization interface [polypeptide binding]; other site 907238001841 active site 907238001842 metal binding site [ion binding]; metal-binding site 907238001843 Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III; Region: DSRM; cd00048 907238001844 dsRNA binding site [nucleotide binding]; other site 907238001845 RNase HI family found mainly in prokaryotes; Region: RNase_HI_prokaryote_like; cd09278 907238001846 RNA/DNA hybrid binding site [nucleotide binding]; other site 907238001847 active site 907238001848 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]; Region: COG2956 907238001849 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]; Region: COG1439 907238001850 SurA N-terminal domain; Region: SurA_N; pfam09312 907238001851 aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated; Region: gatB; PRK05477 907238001852 GatB/GatE catalytic domain; Region: GatB_N; pfam02934 907238001853 GatB domain; Region: GatB_Yqey; smart00845 907238001854 Predicted Zn-dependent peptidases [General function prediction only]; Region: PqqL; COG0612 907238001855 Insulinase (Peptidase family M16); Region: Peptidase_M16; pfam00675 907238001856 Peptidase M16 inactive domain; Region: Peptidase_M16_C; pfam05193 907238001857 hypothetical protein; Provisional; Region: PRK08445 907238001858 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238001859 FeS/SAM binding site; other site 907238001860 Outer membrane protein/protective antigen OMA87 [Cell envelope biogenesis, outer membrane]; Region: COG4775 907238001861 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 907238001862 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 907238001863 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 907238001864 Surface antigen variable number repeat; Region: Surf_Ag_VNR; pfam07244 907238001865 Surface antigen; Region: Bac_surface_Ag; pfam01103 907238001866 hypothetical protein; Provisional; Region: PRK08444 907238001867 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238001868 FeS/SAM binding site; other site 907238001869 nonheme-containing ferritins; Region: Nonheme_Ferritin; cd01055 907238001870 Ferritin-like domain; Region: Ferritin; pfam00210 907238001871 ferroxidase diiron center [ion binding]; other site 907238001872 phosphoserine phosphatase SerB; Region: serB; TIGR00338 907238001873 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 907238001874 motif II; other site 907238001875 Glycosyltransferase family 10 (fucosyltransferase); Region: Glyco_transf_10; pfam00852 907238001876 Uracil-DNA glycosylases (UDG) and related enzymes; Region: UDG_like; cl00483 907238001877 ligand binding site [chemical binding]; other site 907238001878 active site 907238001879 aspartate ammonia-lyase; Provisional; Region: aspA; PRK12273 907238001880 Aspartase; Region: Aspartase; cd01357 907238001881 active sites [active] 907238001882 tetramer interface [polypeptide binding]; other site 907238001883 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Region: murA; TIGR01072 907238001884 UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine =...; Region: UdpNAET; cd01555 907238001885 hinge; other site 907238001886 active site 907238001887 Prokaryotic UGPase catalyses the synthesis of UDP-glucose; Region: UGPase_prokaryotic; cd02541 907238001888 dTDP-glucose pyrophosphorylase [Cell envelope biogenesis, outer membrane]; Region: RfbA; COG1209 907238001889 active site 907238001890 tetramer interface; other site 907238001891 Soluble lytic murein transglycosylase and related regulatory proteins (some contain LysM/invasin domains) [Cell envelope biogenesis, outer membrane]; Region: MltE; COG0741 907238001892 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 907238001893 N-acetyl-D-glucosamine binding site [chemical binding]; other site 907238001894 catalytic residue [active] 907238001895 YGGT family; Region: YGGT; pfam02325 907238001896 glutamylglutaminyl-tRNA synthetase; Provisional; Region: PRK12410 907238001897 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 907238001898 active site 907238001899 HIGH motif; other site 907238001900 nucleotide binding site [chemical binding]; other site 907238001901 catalytic core domain of discriminating glutamyl-tRNA synthetase; Region: GluRS_core; cd00808 907238001902 active site 907238001903 KMSKS motif; other site 907238001904 NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family...; Region: NfsB_like_nitroreductase; cd02149 907238001905 dimer interface [polypeptide binding]; other site 907238001906 FMN binding site [chemical binding]; other site 907238001907 3-hydroxyisobutyrate dehydrogenase and related beta-hydroxyacid dehydrogenases [Lipid metabolism]; Region: MmsB; COG2084 907238001908 6-phosphogluconate dehydrogenase-like protein; Reviewed; Region: PRK09599 907238001909 START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; Region: SRPBCC; cl14643 907238001910 hydrophobic ligand binding site; other site 907238001911 tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]; Region: PcnB; COG0617 907238001912 Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes; Region: NT_ClassII-CCAase; cd05398 907238001913 active site 907238001914 NTP binding site [chemical binding]; other site 907238001915 metal binding triad [ion binding]; metal-binding site 907238001916 Probable RNA and SrmB- binding site of polymerase A; Region: PolyA_pol_RNAbd; pfam12627 907238001917 ExsB is a transcription regulator related protein. It is a subfamily of a Adenosine nucleotide binding superfamily of proteins. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In...; Region: ExsB; cd01995 907238001918 Ligand Binding Site [chemical binding]; other site 907238001919 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238001920 acetolactate synthase 3 catalytic subunit; Validated; Region: PRK06466 907238001921 Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD...; Region: H2MP_MemB-H2up; cd06062 907238001922 nickel binding site [ion binding]; other site 907238001923 putative substrate-binding site; other site 907238001924 Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]; Region: HyaC; COG1969 907238001925 Ni,Fe-hydrogenase I large subunit [Energy production and conversion]; Region: HyaB; COG0374 907238001926 Nickel-dependent hydrogenase; Region: NiFeSe_Hases; pfam00374 907238001927 hydrogenase (NiFe) small subunit (hydA); Region: hydA; TIGR00391 907238001928 NADH ubiquinone oxidoreductase, 20 Kd subunit; Region: Oxidored_q6; pfam01058 907238001929 Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]; Region: MdaB; COG2249 907238001930 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907238001931 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238001932 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907238001933 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907238001934 Sel1-like repeats; Region: SEL1; smart00671 907238001935 Sel1-like repeats; Region: SEL1; smart00671 907238001936 Sel1 repeat; Region: Sel1; cl02723 907238001937 Sel1-like repeats; Region: SEL1; smart00671 907238001938 Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]; Region: DapD; COG2171 907238001939 Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal...; Region: LbH_THP_succinylT_putative; cd04649 907238001940 putative trimer interface [polypeptide binding]; other site 907238001941 putative CoA binding site [chemical binding]; other site 907238001942 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Reviewed; Region: ispG; PRK00366 907238001943 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 907238001944 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated; Region: PRK00694 907238001945 hypothetical protein; Provisional; Region: PRK05839 907238001946 Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine...; Region: AAT_like; cd00609 907238001947 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238001948 homodimer interface [polypeptide binding]; other site 907238001949 catalytic residue [active] 907238001950 UDP-N-acetylmuramate--alanine ligase; Region: murC; TIGR01082 907238001951 Mur ligase family, catalytic domain; Region: Mur_ligase; pfam01225 907238001952 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907238001953 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907238001954 MutS2 family protein; Region: mutS2; TIGR01069 907238001955 ATPase domain of DNA mismatch repair MUTS family; Region: MUTSac; smart00534 907238001956 Walker A/P-loop; other site 907238001957 ATP binding site [chemical binding]; other site 907238001958 Q-loop/lid; other site 907238001959 ABC transporter signature motif; other site 907238001960 Walker B; other site 907238001961 D-loop; other site 907238001962 H-loop/switch region; other site 907238001963 Smr domain; Region: Smr; pfam01713 907238001964 Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers; Region: pyrophosphatase; cd00412 907238001965 dimer interface [polypeptide binding]; other site 907238001966 substrate binding site [chemical binding]; other site 907238001967 metal binding sites [ion binding]; metal-binding site 907238001968 potential frameshift: common BLAST hit: gi|108563027|ref|YP_627343.1| putative lipopolysaccharide biosynthesis protein 907238001969 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907238001970 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cd06532 907238001971 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of...; Region: Glyco_transf_25; cl01298 907238001972 adenylate kinase; Reviewed; Region: adk; PRK00279 907238001973 Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for...; Region: ADK; cd01428 907238001974 AMP-binding site [chemical binding]; other site 907238001975 ATP-AMP (Ap5A)-binding site [chemical binding]; other site 907238001976 aspartyl-tRNA synthetase; Validated; Region: aspS; PRK00476 907238001977 EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND)...; Region: EcAspRS_like_N; cd04317 907238001978 dimer interface [polypeptide binding]; other site 907238001979 anticodon binding site; other site 907238001980 Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of...; Region: AspRS_core; cd00777 907238001981 homodimer interface [polypeptide binding]; other site 907238001982 motif 1; other site 907238001983 active site 907238001984 motif 2; other site 907238001985 GAD domain; Region: GAD; pfam02938 907238001986 Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it...; Region: class_II_aaRS-like_core; cl00268 907238001987 active site 907238001988 motif 3; other site 907238001989 CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and...; Region: CheW_like; cd00588 907238001990 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907238001991 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238001992 active site 907238001993 phosphorylation site [posttranslational modification] 907238001994 intermolecular recognition site; other site 907238001995 dimerization interface [polypeptide binding]; other site 907238001996 NAD-dependent DNA ligase LigA; Validated; Region: ligA; PRK07956 907238001997 NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction...; Region: LIGANc; cd00114 907238001998 nucleotide binding pocket [chemical binding]; other site 907238001999 K-X-D-G motif; other site 907238002000 catalytic site [active] 907238002001 NAD-dependent DNA ligase OB-fold domain; Region: DNA_ligase_OB; pfam03120 907238002002 NAD-dependent DNA ligase C4 zinc finger domain; Region: DNA_ligase_ZBD; pfam03119 907238002003 Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo...; Region: BRCT; cd00027 907238002004 Dimer interface [polypeptide binding]; other site 907238002005 potential frameshift: common BLAST hit: gi|208434533|ref|YP_002266199.1| ABC transporter. ATP-binding protein 907238002006 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002007 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907238002008 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002009 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002010 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002011 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907238002012 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002013 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907238002014 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002015 AcrB/AcrD/AcrF family; Region: ACR_tran; pfam00873 907238002016 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 907238002017 HlyD family secretion protein; Region: HlyD_3; pfam13437 907238002018 Outer membrane efflux protein; Region: OEP; pfam02321 907238002019 Outer membrane efflux protein; Region: OEP; pfam02321 907238002020 Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction...; Region: URO-D; cd00717 907238002021 substrate binding site [chemical binding]; other site 907238002022 active site 907238002023 3-methyladenine DNA glycosylase; Provisional; Region: PRK13913 907238002024 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 907238002025 minor groove reading motif; other site 907238002026 helix-hairpin-helix signature motif; other site 907238002027 active site 907238002028 flagellin A; Reviewed; Region: PRK12584 907238002029 Bacterial flagellin N-terminal helical region; Region: Flagellin_N; pfam00669 907238002030 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907238002031 Flagellin hook IN motif; Region: Flagellin_IN; pfam07196 907238002032 Bacterial flagellin C-terminal helical region; Region: Flagellin_C; pfam00700 907238002033 potential frameshift: common BLAST hit: gi|254779406|ref|YP_003057511.1| ABC-type transport system, permease and ATP-binding protein 907238002034 Methyl-accepting chemotaxis protein (MCP), signaling domain; Region: MCP_signal; cd11386 907238002035 dimer interface [polypeptide binding]; other site 907238002036 putative CheW interface [polypeptide binding]; other site 907238002037 MCP-signal associated domain; Region: MCPsignal_assoc; pfam13682 907238002038 7-keto-8-aminopelargonate synthetase and related enzymes [Coenzyme metabolism]; Region: BioF; COG0156 907238002039 pyridoxal 5'-phosphate binding pocket [chemical binding]; other site 907238002040 catalytic residue [active] 907238002041 Membrane carboxypeptidase (penicillin-binding protein) [Cell envelope biogenesis, outer membrane]; Region: MrcB; COG0744 907238002042 Transglycosylase; Region: Transgly; pfam00912 907238002043 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; cl17760 907238002044 tumor necrosis factor alpha-inducing protein; Reviewed; Region: PRK12303 907238002045 Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]; Region: DsbB; COG1495 907238002046 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907238002047 DNA methylase; Region: N6_N4_Mtase; cl17433 907238002048 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238002049 DNA methylase; Region: N6_N4_Mtase; cl17433 907238002050 Restriction endonuclease [Defense mechanisms]; Region: COG3587 907238002051 Type IV secretory pathway, VirD2 components (relaxase) [Intracellular trafficking and secretion]; Region: VirD2; COG3843 907238002052 tyrosine recombinase XerC; Region: recomb_XerC; TIGR02224 907238002053 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 907238002054 active site 907238002055 catalytic residues [active] 907238002056 DNA binding site [nucleotide binding] 907238002057 Int/Topo IB signature motif; other site 907238002058 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 907238002059 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 907238002060 Toprim-like; Region: Toprim_2; pfam13155 907238002061 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 907238002062 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 907238002063 P-loop; other site 907238002064 Magnesium ion binding site [ion binding]; other site 907238002065 Nucleotidyl transferase of unknown function (DUF1814); Region: DUF1814; pfam08843 907238002066 Topoisomerase IA [DNA replication, recombination, and repair]; Region: TopA; COG0550 907238002067 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 907238002068 active site 907238002069 metal binding site [ion binding]; metal-binding site 907238002070 DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA...; Region: TOP1Ac; cd00186 907238002071 domain I; other site 907238002072 DNA binding groove [nucleotide binding] 907238002073 phosphate binding site [ion binding]; other site 907238002074 domain II; other site 907238002075 domain III; other site 907238002076 nucleotide binding site [chemical binding]; other site 907238002077 catalytic site [active] 907238002078 domain IV; other site 907238002079 Methyltransferase domain; Region: Methyltransf_26; pfam13659 907238002080 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cl17189 907238002081 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 907238002082 DEAD-like helicases superfamily; Region: DEXDc; smart00487 907238002083 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 907238002084 DNA methylase [Transcription / DNA replication, recombination, and repair]; Region: COG4646 907238002085 helicase superfamily c-terminal domain; Region: HELICc; smart00490 907238002086 nucleotide binding region [chemical binding]; other site 907238002087 ATP-binding site [chemical binding]; other site 907238002088 Type IV secretory system Conjugative DNA transfer; Region: T4SS-DNA_transf; pfam02534 907238002089 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 907238002090 Walker A motif; other site 907238002091 ATP binding site [chemical binding]; other site 907238002092 TraM recognition site of TraD and TraG; Region: TraG-D_C; pfam12696 907238002093 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 907238002094 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 907238002095 Walker A motif; other site 907238002096 hexamer interface [polypeptide binding]; other site 907238002097 ATP binding site [chemical binding]; other site 907238002098 Walker B motif; other site 907238002099 Bacterial conjugation TrbI-like protein; Region: TrbI; pfam03743 907238002100 Type IV secretory pathway, VirB9 components [Intracellular trafficking and secretion]; Region: VirB9; COG3504 907238002101 VirB9/CagX/TrbG, a component of the type IV secretion system; Region: VirB9_CagX_TrbG; cd06911 907238002102 VirB7 interaction site; other site 907238002103 VirB8 protein; Region: VirB8; cl01500 907238002104 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 907238002105 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 907238002106 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 907238002107 Walker A motif; other site 907238002108 ATP binding site [chemical binding]; other site 907238002109 Walker B motif; other site 907238002110 TrbC/VIRB2 family; Region: TrbC; pfam04956 907238002111 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238002112 ATP binding site [chemical binding]; other site 907238002113 putative Mg++ binding site [ion binding]; other site 907238002114 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed; Region: oorC; PRK08441 907238002115 2-oxoglutarate ferredoxin oxidoreductase subunit gamma; Validated; Region: PRK08537 907238002116 2-oxoglutarate-acceptor oxidoreductase subunit OorB; Reviewed; Region: oorB; PRK09628 907238002117 Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR...; Region: TPP_OGFOR; cd03375 907238002118 TPP-binding site [chemical binding]; other site 907238002119 2-oxoglutarate-acceptor oxidoreductase subunit OorA; Reviewed; Region: oorA; PRK09627 907238002120 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 907238002121 dimer interface [polypeptide binding]; other site 907238002122 PYR/PP interface [polypeptide binding]; other site 907238002123 TPP binding site [chemical binding]; other site 907238002124 substrate binding site [chemical binding]; other site 907238002125 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed; Region: oorD; PRK09626 907238002126 RPB11 and RPB3 subunits of RNA polymerase; Region: RNAP_RPB11_RPB3; cl11409 907238002127 Aminodeoxychorismate lyase [Coenzyme transport and metabolism]; Region: COG1559 907238002128 proteins similar to Escherichia coli yceG; Region: yceG_like; cd08010 907238002129 dimerization interface [polypeptide binding]; other site 907238002130 Protein of unknown function; Region: DUF3971; pfam13116 907238002131 AsmA-like C-terminal region; Region: AsmA_1; pfam13109 907238002132 Fe2+ transport system protein A [Inorganic ion transport and metabolism]; Region: FeoA; COG1918 907238002133 Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]; Region: Nth; COG0177 907238002134 endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases; Region: ENDO3c; cd00056 907238002135 minor groove reading motif; other site 907238002136 helix-hairpin-helix signature motif; other site 907238002137 substrate binding pocket [chemical binding]; other site 907238002138 active site 907238002139 iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3); Region: FES; smart00525 907238002140 flagellar motor switch protein; Validated; Region: PRK08433 907238002141 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 907238002142 TonB family C-terminal domain; Region: tonB_Cterm; TIGR01352 907238002143 Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is...; Region: DHOase; cd01294 907238002144 active site 907238002145 substrate binding pocket [chemical binding]; other site 907238002146 dimer interface [polypeptide binding]; other site 907238002147 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism]; Region: COG4692 907238002148 BNR repeat-like domain; Region: BNR_2; pfam13088 907238002149 Phosphoglycerol transferase and related proteins, alkaline phosphatase superfamily [Cell envelope biogenesis, outer membrane]; Region: MdoB; COG1368 907238002150 Sulfatase; Region: Sulfatase; pfam00884 907238002151 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional; Region: PRK14191 907238002152 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; Region: THF_DHG_CYH; pfam00763 907238002153 NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase; Region: NAD_bind_m-THF_DH_Cyclohyd; cd01080 907238002154 homodimer interface [polypeptide binding]; other site 907238002155 NADP binding site [chemical binding]; other site 907238002156 substrate binding site [chemical binding]; other site 907238002157 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 907238002158 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 907238002159 Catalytic site [active] 907238002160 The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are...; Region: S26_SPase_I; cd06530 907238002161 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the...; Region: S2P-M50_like_1; cd06158 907238002162 Peptidase family M50; Region: Peptidase_M50; pfam02163 907238002163 active site 907238002164 putative substrate binding region [chemical binding]; other site 907238002165 Ribose/Galactose Isomerase; Region: LacAB_rpiB; cl00485 907238002166 signal peptidase I, bacterial type; Region: sigpep_I_bact; TIGR02227 907238002167 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907238002168 active site 907238002169 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 907238002170 multifunctional aminopeptidase A; Provisional; Region: PRK00913 907238002171 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and...; Region: Peptidase_M17; cd00433 907238002172 interface (dimer of trimers) [polypeptide binding]; other site 907238002173 Substrate-binding/catalytic site; other site 907238002174 Zn-binding sites [ion binding]; other site 907238002175 GTP-binding protein YchF; Reviewed; Region: PRK09601 907238002176 YchF GTPase; Region: YchF; cd01900 907238002177 G1 box; other site 907238002178 GTP/Mg2+ binding site [chemical binding]; other site 907238002179 Switch I region; other site 907238002180 G2 box; other site 907238002181 Switch II region; other site 907238002182 G3 box; other site 907238002183 G4 box; other site 907238002184 G5 box; other site 907238002185 TGS_YchF_C: This subfamily represents TGS domain-containing YchF GTP-binding protein, a universally conserved GTPase whose function is unknown. The N-terminal domain of the YchF protein belongs to the Obg-like family of GTPases, and some members of the...; Region: TGS_YchF_C; cd04867 907238002186 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238002187 FeS/SAM binding site; other site 907238002188 Domain of unknown function (DUF4008); Region: DUF4008; pfam13186 907238002189 Predicted permease, member of the PurR regulon [General function prediction only]; Region: yhhT; COG0628 907238002190 Domain of unknown function DUF20; Region: UPF0118; pfam01594 907238002191 diaminopimelate epimerase; Region: DapF; TIGR00652 907238002192 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 907238002193 Diaminopimelate epimerase; Region: DAP_epimerase; pfam01678 907238002194 Predicted membrane protein [Function unknown]; Region: COG3059 907238002195 30S ribosomal protein S21; Reviewed; Region: rpsU; PRK00270 907238002196 3-ketoacyl-(acyl-carrier-protein) reductase; Validated; Region: fabG; PRK05653 907238002197 Rossmann-fold NAD(P)(+)-binding proteins; Region: NADB_Rossmann; cl09931 907238002198 NAD(P) binding site [chemical binding]; other site 907238002199 active site 907238002200 acyl carrier protein; Provisional; Region: acpP; PRK00982 907238002201 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed; Region: PRK08439 907238002202 Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen...; Region: KAS_I_II; cd00834 907238002203 dimer interface [polypeptide binding]; other site 907238002204 active site 907238002205 acetyl-CoA carboxylase, carboxyl transferase, alpha subunit; Region: accA; TIGR00513 907238002206 acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional; Region: accA; CHL00198 907238002207 rRNA methylase, putative, group 3; Region: rRNA_methyl_3; TIGR00186 907238002208 RNA 2'-O ribose methyltransferase substrate binding; Region: SpoU_sub_bind; smart00967 907238002209 SpoU rRNA Methylase family; Region: SpoU_methylase; pfam00588 907238002210 Predicted methyltransferases [General function prediction only]; Region: COG0313 907238002211 Ribosomal RNA small subunit methyltransferase I, also known as rRNA (cytidine-2'-O-)-methyltransferase RsmI; Region: RsmI; cd11648 907238002212 putative SAM binding site [chemical binding]; other site 907238002213 putative homodimer interface [polypeptide binding]; other site 907238002214 Ribosomal protein L31; Region: Ribosomal_L31; pfam01197 907238002215 transcription termination factor Rho; Provisional; Region: rho; PRK09376 907238002216 Rho termination factor, N-terminal domain; Region: Rho_N; pfam07498 907238002217 Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA...; Region: Rho_CSD; cd04459 907238002218 RNA binding site [nucleotide binding]; other site 907238002219 Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal domain of the OB fold, which is responsible for binding to cysteine rich nucleotides. This alignment is of the...; Region: rho_factor; cd01128 907238002220 multimer interface [polypeptide binding]; other site 907238002221 Walker A motif; other site 907238002222 ATP binding site [chemical binding]; other site 907238002223 Walker B motif; other site 907238002224 glutamate racemase; Region: glut_race; TIGR00067 907238002225 CagA exotoxin; Region: CagA; pfam03507 907238002226 CagA exotoxin; Region: CagA; pfam03507 907238002227 type IV secretion/conjugal transfer ATPase, VirB4 family; Region: VirB4_CagE; TIGR00929 907238002228 CagE, TrbE, VirB family, component of type IV transporter system; Region: CagE_TrbE_VirB; pfam03135 907238002229 prolyl-tRNA synthetase; Provisional; Region: PRK08661 907238002230 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK06945 907238002231 Cag pathogenicity island protein Cag12; Region: Cag12; pfam13117 907238002232 Type IV secretory pathway, component VirB8 [Intracellular trafficking and secretion]; Region: VirB8; COG3736 907238002233 potential frameshift: common BLAST hit: gi|308182682|ref|YP_003926809.1| cag pathogenicity island protein X 907238002234 DC-EC Repeat; Region: CagY_M; pfam07337 907238002235 DC-EC Repeat; Region: CagY_M; pfam07337 907238002236 DC-EC Repeat; Region: CagY_M; pfam07337 907238002237 DC-EC Repeat; Region: CagY_M; pfam07337 907238002238 DC-EC Repeat; Region: CagY_M; pfam07337 907238002239 DC-EC Repeat; Region: CagY_M; pfam07337 907238002240 DC-EC Repeat; Region: CagY_M; pfam07337 907238002241 DC-EC Repeat; Region: CagY_M; pfam07337 907238002242 Type IV secretory pathway, VirB10 components [Intracellular trafficking and secretion]; Region: VirB10; COG2948 907238002243 CagZ; Region: CagZ; pfam09053 907238002244 P-type DNA transfer ATPase VirB11; Region: VirB11; TIGR02788 907238002245 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 907238002246 ATP binding site [chemical binding]; other site 907238002247 Walker A motif; other site 907238002248 hexamer interface [polypeptide binding]; other site 907238002249 Walker B motif; other site 907238002250 Type IV secretory pathway, VirD4 components [Intracellular trafficking and secretion]; Region: VirD4; COG3505 907238002251 The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome. They contain an ATP binding domain. VirD4 is involved in DNA transfer...; Region: TraG_VirD4; cd01126 907238002252 Walker A motif; other site 907238002253 ATP binding site [chemical binding]; other site 907238002254 Walker B motif; other site 907238002255 Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]; Region: TopA; COG0551 907238002256 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907238002257 Sel1-like repeats; Region: SEL1; smart00671 907238002258 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3034 907238002259 GTPase [General function prediction only]; Region: Era; COG1159 907238002260 E. coli Ras-like protein (Era) is a multifunctional GTPase; Region: Era; cd04163 907238002261 G1 box; other site 907238002262 GTP/Mg2+ binding site [chemical binding]; other site 907238002263 Switch I region; other site 907238002264 G2 box; other site 907238002265 Switch II region; other site 907238002266 G3 box; other site 907238002267 G4 box; other site 907238002268 G5 box; other site 907238002269 KH domain; Region: KH_2; pfam07650 907238002270 ATP-dependent protease ATP-binding subunit HslU; Provisional; Region: hslU; PRK05201 907238002271 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238002272 Walker A motif; other site 907238002273 ATP binding site [chemical binding]; other site 907238002274 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238002275 Walker B motif; other site 907238002276 arginine finger; other site 907238002277 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 907238002278 Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the...; Region: protease_HslV; cd01913 907238002279 active site 907238002280 HslU subunit interaction site [polypeptide binding]; other site 907238002281 ribosomal protein L9; Region: L9; TIGR00158 907238002282 Ribosomal protein L9, N-terminal domain; Region: Ribosomal_L9_N; pfam01281 907238002283 Ribosomal protein L9, C-terminal domain; Region: Ribosomal_L9_C; pfam03948 907238002284 glutamine synthetase, type I; Region: GlnA; TIGR00653 907238002285 Glutamine synthetase, beta-Grasp domain; Region: Gln-synt_N; pfam03951 907238002286 Glutamine synthetase, catalytic domain; Region: Gln-synt_C; pfam00120 907238002287 dihydrodipicolinate reductase; Region: dapB; TIGR00036 907238002288 Dihydrodipicolinate reductase, N-terminus; Region: DapB_N; pfam01113 907238002289 Dihydrodipicolinate reductase, C-terminus; Region: DapB_C; pfam05173 907238002290 FAD binding domain; Region: FAD_binding_4; pfam01565 907238002291 glycolate oxidase, subunit GlcD; Region: glcD; TIGR00387 907238002292 Protein-interacting Bro1-like domain of mammalian Alix and related domains; Region: BRO1_Alix_like; cl14649 907238002293 nudix-type nucleoside diphosphatase, YffH/AdpP family; Region: TIGR00052 907238002294 ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. Like other members of the Nudix hydrolase superfamily, it requires a divalent cation, such as Mg2+; Region: ADPRase_NUDT5; cd03424 907238002295 dimer interface [polypeptide binding]; other site 907238002296 ADP-ribose binding site [chemical binding]; other site 907238002297 active site 907238002298 nudix motif; other site 907238002299 metal binding site [ion binding]; metal-binding site 907238002300 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907238002301 Peptidase family M23; Region: Peptidase_M23; pfam01551 907238002302 R.Pab1 restriction endonuclease; Region: RE_R_Pab1; pfam09522 907238002303 DNA gyrase subunit B; Provisional; Region: gyrB; PRK14939 907238002304 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 907238002305 Mg2+ binding site [ion binding]; other site 907238002306 G-X-G motif; other site 907238002307 TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are; Region: TopoII_Trans_DNA_gyrase; cd00822 907238002308 anchoring element; other site 907238002309 dimer interface [polypeptide binding]; other site 907238002310 ATP binding site [chemical binding]; other site 907238002311 TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the...; Region: TOPRIM_TopoIIA_GyrB; cd03366 907238002312 active site 907238002313 putative metal-binding site [ion binding]; other site 907238002314 DNA gyrase B subunit, carboxyl terminus; Region: DNA_gyraseB_C; pfam00986 907238002315 DNA polymerase III, beta subunit; Region: dnan; TIGR00663 907238002316 Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric...; Region: beta_clamp; cd00140 907238002317 putative DNA binding surface [nucleotide binding]; other site 907238002318 dimer interface [polypeptide binding]; other site 907238002319 beta-clamp/translesion DNA polymerase binding surface; other site 907238002320 beta-clamp/clamp loader binding surface; other site 907238002321 The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among...; Region: OMPLA; cd00541 907238002322 dimerization interface [polypeptide binding]; other site 907238002323 substrate binding site [chemical binding]; other site 907238002324 active site 907238002325 calcium binding site [ion binding]; other site 907238002326 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 907238002327 Na2 binding site [ion binding]; other site 907238002328 putative substrate binding site 1 [chemical binding]; other site 907238002329 Na binding site 1 [ion binding]; other site 907238002330 putative substrate binding site 2 [chemical binding]; other site 907238002331 solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain; Region: SLC6sbd_Tyt1-Like; cd10336 907238002332 Na2 binding site [ion binding]; other site 907238002333 putative substrate binding site 1 [chemical binding]; other site 907238002334 Na binding site 1 [ion binding]; other site 907238002335 putative substrate binding site 2 [chemical binding]; other site 907238002336 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites; Region: 4HBT; cd00586 907238002337 active site 907238002338 Protein of unknown function (DUF493); Region: DUF493; pfam04359 907238002339 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional; Region: murD; PRK03815 907238002340 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907238002341 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907238002342 phospho-N-acetylmuramoyl-pentapeptide-transferase; Region: mraY; TIGR00445 907238002343 Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of...; Region: GT_MraY; cd06852 907238002344 Mg++ binding site [ion binding]; other site 907238002345 putative catalytic motif [active] 907238002346 putative substrate binding site [chemical binding]; other site 907238002347 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907238002348 50S ribosomal protein L28; Reviewed; Region: rpmB; PRK00359 907238002349 Cation transport protein; Region: TrkH; cl17365 907238002350 Kef-type K+ transport systems, predicted NAD-binding component [Inorganic ion transport and metabolism]; Region: Kch; COG1226 907238002351 TrkA-N domain; Region: TrkA_N; pfam02254 907238002352 TrkA-C domain; Region: TrkA_C; pfam02080 907238002353 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238002354 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238002355 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238002356 Holliday junction DNA helicase, RuvA subunit; Region: ruvA; TIGR00084 907238002357 RuvA N terminal domain; Region: RuvA_N; pfam01330 907238002358 RuvA, C-terminal domain; Region: RuvA_C; pfam07499 907238002359 MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins; Region: MATE_MurJ_like; cd13123 907238002360 MviN-like protein; Region: MVIN; pfam03023 907238002361 cysteinyl-tRNA synthetase; Validated; Region: cysS; PRK00260 907238002362 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 907238002363 active site 907238002364 HIGH motif; other site 907238002365 catalytic core domain of cysteinyl tRNA synthetase; Region: CysRS_core; cd00672 907238002366 KMSKS motif; other site 907238002367 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 907238002368 tRNA binding surface [nucleotide binding]; other site 907238002369 anticodon binding site; other site 907238002370 Vacuolating cyotoxin; Region: VacA; pfam02691 907238002371 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907238002372 potential frameshift: common BLAST hit: gi|108563293|ref|YP_627609.1| lipopolysaccharide 1,2-glycosyltransferase 907238002373 ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]; Region: FepC; COG1120 907238002374 ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins; Region: ABC_Iron-Siderophores_B12_Hemin; cd03214 907238002375 Walker A/P-loop; other site 907238002376 ATP binding site [chemical binding]; other site 907238002377 Q-loop/lid; other site 907238002378 ABC transporter signature motif; other site 907238002379 Walker B; other site 907238002380 D-loop; other site 907238002381 H-loop/switch region; other site 907238002382 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cl00462 907238002383 iron-hydroxamate transporter permease subunit; Provisional; Region: PRK10577 907238002384 Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of...; Region: TM_ABC_iron-siderophores_like; cd06550 907238002385 ABC-ATPase subunit interface; other site 907238002386 dimer interface [polypeptide binding]; other site 907238002387 putative PBP binding regions; other site 907238002388 short chain dehydrogenase; Validated; Region: PRK06182 907238002389 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs; Region: 17beta-HSD-like_SDR_c; cd05374 907238002390 NADP binding site [chemical binding]; other site 907238002391 active site 907238002392 steroid binding site; other site 907238002393 Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis; Region: BFIT_BACH; cd03442 907238002394 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 907238002395 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041 907238002396 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002397 hydrogenase expression/formation protein HypD; Region: hypD; TIGR00075 907238002398 hydrogenase isoenzymes formation protein HypD; Provisional; Region: PRK15062 907238002399 Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]; Region: HypC; COG0298 907238002400 hydrogenase accessory protein HypB; Region: hypB; TIGR00073 907238002401 ATPases associated with a variety of cellular activities; Region: AAA; smart00382 907238002402 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]; Region: COG1917 907238002403 acetate kinase A/propionate kinase 2; Reviewed; Region: PRK00180 907238002404 propionate/acetate kinase; Provisional; Region: PRK12379 907238002405 BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]; Region: Pta; COG0857 907238002406 phosphotransacetylase; Reviewed; Region: eutD; PRK09653 907238002407 Flagellar hook-length control protein FliK; Region: Flg_hook; pfam02120 907238002408 flagellar basal body rod modification protein; Reviewed; Region: flgD; PRK05842 907238002409 Flagellar hook capping protein - N-terminal region; Region: FlgD; pfam03963 907238002410 FlgD Tudor-like domain; Region: FLgD_tudor; pfam13861 907238002411 flagellar hook protein FlgE; Validated; Region: flgE; PRK05841 907238002412 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907238002413 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG0827 907238002414 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238002415 S-adenosylmethionine binding site [chemical binding]; other site 907238002416 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 907238002417 Part of AAA domain; Region: AAA_19; pfam13245 907238002418 Family description; Region: UvrD_C_2; pfam13538 907238002419 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002420 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002421 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238002422 potential frameshift: common BLAST hit: gi|383749421|ref|YP_005424524.1| iron-regulated outer membrane protein 907238002423 TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein; Region: TonB-hemlactrns; TIGR01786 907238002424 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 907238002425 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 907238002426 Telomere recombination; Region: Sua5_yciO_yrdC; cl00305 907238002427 carbamoyl phosphate synthase large subunit; Reviewed; Region: carB; PRK05294 907238002428 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 907238002429 ATP-grasp domain; Region: ATP-grasp_4; cl17255 907238002430 Carbamoyl-phosphate synthetase large chain, oligomerisation domain; Region: CPSase_L_D3; pfam02787 907238002431 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 907238002432 ATP-grasp domain; Region: ATP-grasp_4; cl17255 907238002433 Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways...; Region: MGS_CPS_II; cd01424 907238002434 IMP binding site; other site 907238002435 dimer interface [polypeptide binding]; other site 907238002436 interdomain contacts; other site 907238002437 partial ornithine binding site; other site 907238002438 Bacterial BAX inhibitor (BI)-1/YccA-like proteins; Region: BI-1-like_bacterial; cd10432 907238002439 Integral membrane protein, interacts with FtsH [General function prediction only]; Region: COG0670 907238002440 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 907238002441 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 907238002442 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 907238002443 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002444 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002445 PPE-repeat proteins [Cell motility and secretion]; Region: COG5651 907238002446 Putative vacuolating cytotoxin; Region: VacA2; pfam03077 907238002447 Autotransporter beta-domain; Region: Autotransporter; pfam03797 907238002448 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002449 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one...; Region: 4Oxalocrotonate_Tautomerase; cd00491 907238002450 active site 1 [active] 907238002451 dimer interface [polypeptide binding]; other site 907238002452 hexamer interface [polypeptide binding]; other site 907238002453 active site 2 [active] 907238002454 recombination protein RecR; Region: recR; TIGR00615 907238002455 RecR protein; Region: RecR; pfam02132 907238002456 TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a...; Region: TOPRIM_recR; cd01025 907238002457 putative active site [active] 907238002458 putative metal-binding site [ion binding]; other site 907238002459 tetramer interface [polypeptide binding]; other site 907238002460 tRNA pseudouridine synthase, TruD family; Region: tRNA_TruD_broad; TIGR00094 907238002461 Pseudouridine synthase, similar to Escherichia coli TruD; Region: PseudoU_synth_EcTruD; cd02575 907238002462 Permutation of conserved domain; other site 907238002463 active site 907238002464 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 907238002465 heat shock protein HtpX; Provisional; Region: PRK02870 907238002466 GTP cyclohydrolase I; Region: folE; TIGR00063 907238002467 GTP cyclohydrolase I; Provisional; Region: PLN03044 907238002468 active site 907238002469 Geranylgeranyl pyrophosphate synthase [Coenzyme metabolism]; Region: IspA; COG0142 907238002470 Trans-Isoprenyl Diphosphate Synthases, head-to-tail; Region: Trans_IPPS_HT; cd00685 907238002471 substrate binding pocket [chemical binding]; other site 907238002472 chain length determination region; other site 907238002473 substrate-Mg2+ binding site; other site 907238002474 catalytic residues [active] 907238002475 aspartate-rich region 1; other site 907238002476 active site lid residues [active] 907238002477 aspartate-rich region 2; other site 907238002478 5'(3')-nucleotidase/polyphosphatase; Provisional; Region: surE; PRK00346 907238002479 6-pyruvoyl-tetrahydropterin synthase [Coenzyme metabolism]; Region: COG0720 907238002480 Organic radical activating enzymes [Posttranslational modification, protein turnover, chaperones]; Region: NrdG; COG0602 907238002481 putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE; Region: rSAM_QueE_Ecoli; TIGR04322 907238002482 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cd04301 907238002483 Coenzyme A binding pocket [chemical binding]; other site 907238002484 N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate; Region: NAT_SF; cl17182 907238002485 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002486 metabolite-proton symporter; Region: 2A0106; TIGR00883 907238002487 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 907238002488 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238002489 dimer interface [polypeptide binding]; other site 907238002490 conserved gate region; other site 907238002491 putative PBP binding loops; other site 907238002492 ABC-ATPase subunit interface; other site 907238002493 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 907238002494 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 907238002495 substrate binding pocket [chemical binding]; other site 907238002496 membrane-bound complex binding site; other site 907238002497 hinge residues; other site 907238002498 alanine racemase; Region: alr; TIGR00492 907238002499 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; Region: PLPDE_III_AR; cd00430 907238002500 active site 907238002501 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907238002502 dimer interface [polypeptide binding]; other site 907238002503 substrate binding site [chemical binding]; other site 907238002504 catalytic residues [active] 907238002505 Na+/alanine symporter [Amino acid transport and metabolism]; Region: AlsT; COG1115 907238002506 amino acid carrier protein; Region: agcS; TIGR00835 907238002507 Glycine/D-amino acid oxidases (deaminating) [Amino acid transport and metabolism]; Region: DadA; COG0665 907238002508 Streptococcal 67 kDa myosin-cross-reactive antigen like family; Region: Strep_67kDa_ant; cl17487 907238002509 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no...; Region: YjgF_YER057c_UK114_family; cd00448 907238002510 homotrimer interaction site [polypeptide binding]; other site 907238002511 putative active site [active] 907238002512 Na+/H+ antiporter [Energy production and conversion]; Region: NhaC; COG1757 907238002513 Uncharacterized conserved protein [Function unknown]; Region: COG1576 907238002514 acetyl-CoA carboxylase, carboxyl transferase, beta subunit; Region: accD; TIGR00515 907238002515 malonate decarboxylase subunit beta; Reviewed; Region: PRK07189; cl17682 907238002516 putative recombination protein RecO; Provisional; Region: PRK13908 907238002517 competence/damage-inducible protein CinA C-terminal domain; Region: cinA_cterm; TIGR00199 907238002518 potential frameshift: common BLAST hit: gi|108563363|ref|YP_627679.1| oxygen-insensitive NADPH nitroreductase 907238002519 prolipoprotein diacylglyceryl transferase; Region: lgt; TIGR00544 907238002520 Pseudouridylate synthases, 23S RNA-specific [Translation, ribosomal structure and biogenesis]; Region: RluA; COG0564 907238002521 Pseudouridine synthase, RsuA/RluD family; Region: PseudoU_synth_RluCD_like; cd02869 907238002522 active site 907238002523 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed; Region: PRK05749 907238002524 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase); Region: Glycos_transf_N; pfam04413 907238002525 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 907238002526 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]; Region: COG1579 907238002527 Putative zinc ribbon domain; Region: DUF164; pfam02591 907238002528 dinuclear metal center protein, YbgI/SA1388 family; Region: YbgI_SA1388; TIGR00486 907238002529 Uncharacterized conserved protein [Function unknown]; Region: COG0327 907238002530 Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the...; Region: GlyRS_alpha_core; cd00733 907238002531 dimer interface [polypeptide binding]; other site 907238002532 motif 1; other site 907238002533 active site 907238002534 motif 2; other site 907238002535 motif 3; other site 907238002536 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Validated; Region: gpsA; PRK00094 907238002537 NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; Region: NAD_Gly3P_dh_N; pfam01210 907238002538 NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus; Region: NAD_Gly3P_dh_C; pfam07479 907238002539 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 907238002540 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 907238002541 G1 box; other site 907238002542 GTP/Mg2+ binding site [chemical binding]; other site 907238002543 G2 box; other site 907238002544 Switch I region; other site 907238002545 G3 box; other site 907238002546 Switch II region; other site 907238002547 G4 box; other site 907238002548 G5 box; other site 907238002549 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 907238002550 G1 box; other site 907238002551 GTP/Mg2+ binding site [chemical binding]; other site 907238002552 G2 box; other site 907238002553 Switch I region; other site 907238002554 Predicted GTPases (dynamin-related) [General function prediction only]; Region: COG0699 907238002555 Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases); Region: Ras_like_GTPase; cl17170 907238002556 G3 box; other site 907238002557 Switch II region; other site 907238002558 G4 box; other site 907238002559 Uncharacterized virulence-associated protein D [Function unknown]; Region: VapD; COG3309 907238002560 Protein of unknown function (DUF3240); Region: DUF3240; pfam11582 907238002561 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 907238002562 Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid...; Region: lipoyl_domain; cd06849 907238002563 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 907238002564 Outer membrane efflux protein; Region: OEP; pfam02321 907238002565 Outer membrane efflux protein; Region: OEP; pfam02321 907238002566 glycyl-tRNA synthetase, tetrameric type, beta subunit; Region: glyS; TIGR00211 907238002567 phosphoglyceromutase; Provisional; Region: PRK05434 907238002568 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; Region: pgm_bpd_ind; TIGR01307 907238002569 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit; Region: gatC; TIGR00135 907238002570 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional; Region: PRK05964 907238002571 Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase; Region: OAT_like; cd00610 907238002572 inhibitor-cofactor binding pocket; inhibition site 907238002573 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238002574 catalytic residue [active] 907238002575 SurA N-terminal domain; Region: SurA_N_3; cl07813 907238002576 peptidylprolyl isomerase; Provisional; Region: prsA; PRK00059 907238002577 PPIC-type PPIASE domain; Region: Rotamase_2; pfam13145 907238002578 cell division protein FtsA; Region: ftsA; TIGR01174 907238002579 Cell division protein FtsA; Region: FtsA; smart00842 907238002580 Cell division protein FtsA; Region: FtsA; pfam14450 907238002581 cell division protein FtsZ; Validated; Region: PRK09330 907238002582 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at...; Region: FtsZ_type1; cd02201 907238002583 nucleotide binding site [chemical binding]; other site 907238002584 SulA interaction site; other site 907238002585 Mechanosensitive ion channel; Region: MS_channel; pfam00924 907238002586 AAA domain; Region: AAA_33; pfam13671 907238002587 potential frameshift: common BLAST hit: gi|210135186|ref|YP_002301625.1| phage/colicin/tellurite resistance cluster protein TerY 907238002588 potential protein location (hypothetical protein HPIN_05050 [Helicobacter pylori India7]) that overlaps RNA (5S ribosomal RNA) 907238002589 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907238002590 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238002591 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238002592 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907238002593 Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]; Region: RecJ; COG0608 907238002594 DHH family; Region: DHH; pfam01368 907238002595 Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]; Region: SpeA; COG1166 907238002596 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase; Region: PLPDE_III_ADC; cd06830 907238002597 active site 907238002598 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907238002599 catalytic residues [active] 907238002600 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; Region: PLPDE_III; cl00261 907238002601 Glycosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaG; COG0438 907238002602 This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1; Region: GT1_UGDG_like; cd03817 907238002603 putative ADP-binding pocket [chemical binding]; other site 907238002604 The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated...; Region: hot_dog; cd03440 907238002605 active site 2 [active] 907238002606 active site 1 [active] 907238002607 Methyltransferase domain; Region: Methyltransf_23; pfam13489 907238002608 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238002609 S-adenosylmethionine binding site [chemical binding]; other site 907238002610 UDP-N-acetylmuramoylalanyl-D-glutamate--2, 6-diaminopimelate ligase; Provisional; Region: murE; PRK00139 907238002611 methionyl-tRNA synthetase; Reviewed; Region: PRK12267 907238002612 catalytic core domain of methioninyl-tRNA synthetases; Region: MetRS_core; cd00814 907238002613 active site 907238002614 HIGH motif; other site 907238002615 KMSKS motif; other site 907238002616 Anticodon-binding domain of methionyl tRNA synthetases; Region: Anticodon_Ia_Met; cd07957 907238002617 anticodon binding site; other site 907238002618 tRNA binding surface [nucleotide binding]; other site 907238002619 tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine...; Region: tRNA_bind_EcMetRS_like; cd02800 907238002620 dimer interface [polypeptide binding]; other site 907238002621 putative tRNA-binding site [nucleotide binding]; other site 907238002622 Mycolic acid cyclopropane synthetase; Region: CMAS; pfam02353 907238002623 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238002624 S-adenosylmethionine binding site [chemical binding]; other site 907238002625 Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]; Region: MscS; COG0668 907238002626 Mechanosensitive ion channel; Region: MS_channel; pfam00924 907238002627 potential protein location (hypothetical protein HPIN_05130 [Helicobacter pylori India7]) that overlaps RNA (tRNA-P) 907238002628 Neuraminyllactose-binding hemagglutinin precursor (NLBH); Region: NLBH; pfam05211 907238002629 GMP synthase; Reviewed; Region: guaA; PRK00074 907238002630 Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase; Region: GATase1_GMP_Synthase; cd01742 907238002631 AMP/PPi binding site [chemical binding]; other site 907238002632 candidate oxyanion hole; other site 907238002633 catalytic triad [active] 907238002634 potential glutamine specificity residues [chemical binding]; other site 907238002635 The C-terminal domain of GMP synthetase. It contains two subdomains; the ATP pyrophosphatase domain which closes to the N-termial and the dimerization domain at C-terminal end. The ATP-PPase is a twisted, five-stranded parallel beta-sheet sandwiched...; Region: GMP_synthase_C; cd01997 907238002636 ATP Binding subdomain [chemical binding]; other site 907238002637 Ligand Binding sites [chemical binding]; other site 907238002638 Dimerization subdomain; other site 907238002639 potential frameshift: common BLAST hit: gi|298735955|ref|YP_003728480.1| trimethylamine-N-oxide reductase 907238002640 Protein of unknown function (DUF3972); Region: DUF3972; pfam13118 907238002641 Selenocysteine lyase/Cysteine desulfurase [Posttranslational modification, protein turnover, chaperones]; Region: csdA; COG0520 907238002642 Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the...; Region: AAT_I; cl00321 907238002643 catalytic residue [active] 907238002644 Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a...; Region: PKCI_related; cd01276 907238002645 nucleotide binding site/active site [active] 907238002646 HIT family signature motif; other site 907238002647 catalytic residue [active] 907238002648 phenylalanyl-tRNA synthetase subunit alpha; Validated; Region: pheS; PRK00488 907238002649 Aminoacyl tRNA synthetase class II, N-terminal domain; Region: Phe_tRNA-synt_N; pfam02912 907238002650 Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible...; Region: PheRS_alpha_core; cd00496 907238002651 dimer interface [polypeptide binding]; other site 907238002652 motif 1; other site 907238002653 active site 907238002654 motif 2; other site 907238002655 motif 3; other site 907238002656 phenylalanyl-tRNA synthetase subunit beta; Reviewed; Region: pheT; PRK00629 907238002657 tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate...; Region: tRNA_bind_bactPheRS; cd02796 907238002658 putative tRNA-binding site [nucleotide binding]; other site 907238002659 tRNA synthetase B5 domain; Region: B5; pfam03484 907238002660 Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an...; Region: PheRS_beta_core; cd00769 907238002661 dimer interface [polypeptide binding]; other site 907238002662 motif 1; other site 907238002663 motif 3; other site 907238002664 motif 2; other site 907238002665 Ferredoxin-fold anticodon binding domain; Region: FDX-ACB; pfam03147 907238002666 EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form...; Region: EPSP_synthase; cd01556 907238002667 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional; Region: PRK02427 907238002668 hinge; other site 907238002669 active site 907238002670 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed; Region: ispH; PRK01045 907238002671 LytB protein; Region: LYTB; pfam02401 907238002672 ribosomal protein S1; Region: rpsA; TIGR00717 907238002673 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture...; Region: S1_RPS1_repeat_ec2_hs2; cd04465 907238002674 RNA binding site [nucleotide binding]; other site 907238002675 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cd00164 907238002676 RNA binding site [nucleotide binding]; other site 907238002677 S1 RNA binding domain; Region: S1; pfam00575 907238002678 RNA binding site [nucleotide binding]; other site 907238002679 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cl09927 907238002680 RNA binding site [nucleotide binding]; other site 907238002681 S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain; Region: S1_like; cd00164 907238002682 RNA binding site [nucleotide binding]; other site 907238002683 D-3-phosphoglycerate dehydrogenase; Region: PGDH; TIGR01327 907238002684 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Region: PGDH_4; cd12173 907238002685 ligand binding site [chemical binding]; other site 907238002686 NAD binding site [chemical binding]; other site 907238002687 dimerization interface [polypeptide binding]; other site 907238002688 catalytic site [active] 907238002689 C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); Region: ACT_3PGDH-xct; cd04902 907238002690 putative L-serine binding site [chemical binding]; other site 907238002691 menaquinone biosynthesis decarboxylase, SCO4490 family; Region: mena_SCO4490; TIGR03701 907238002692 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Region: UbiD; cl00311 907238002693 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins; Region: PLPDE_III_YBL036c_like; cd00635 907238002694 pyridoxal 5'-phosphate (PLP) binding site [chemical binding]; other site 907238002695 catalytic residue [active] 907238002696 Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; Region: MPP_YbbF-LpxH; cd07398 907238002697 putative active site [active] 907238002698 putative metal binding site [ion binding]; other site 907238002699 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 907238002700 putative CheA interaction surface; other site 907238002701 FOG: CheY-like receiver [Signal transduction mechanisms]; Region: CheY; COG0784 907238002702 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238002703 active site 907238002704 phosphorylation site [posttranslational modification] 907238002705 intermolecular recognition site; other site 907238002706 dimerization interface [polypeptide binding]; other site 907238002707 Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is...; Region: HPT; cd00088 907238002708 putative binding surface; other site 907238002709 active site 907238002710 Chemotaxis protein histidine kinase and related kinases [Cell motility and secretion / Signal transduction mechanisms]; Region: CheA; COG0643 907238002711 Signal transducing histidine kinase, homodimeric domain; Region: H-kinase_dim; pfam02895 907238002712 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 907238002713 ATP binding site [chemical binding]; other site 907238002714 Mg2+ binding site [ion binding]; other site 907238002715 G-X-G motif; other site 907238002716 CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling...; Region: CheA_reg; cd00731 907238002717 Response regulator receiver domain; Region: Response_reg; pfam00072 907238002718 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238002719 active site 907238002720 phosphorylation site [posttranslational modification] 907238002721 intermolecular recognition site; other site 907238002722 dimerization interface [polypeptide binding]; other site 907238002723 CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together...; Region: CheW; cd00732 907238002724 putative CheA interaction surface; other site 907238002725 Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a...; Region: PRX_Atyp2cys; cd03014 907238002726 dimer interface [polypeptide binding]; other site 907238002727 catalytic triad [active] 907238002728 peroxidatic and resolving cysteines [active] 907238002729 Superoxide dismutase [Inorganic ion transport and metabolism]; Region: SodA; COG0605 907238002730 Iron/manganese superoxide dismutases, alpha-hairpin domain; Region: Sod_Fe_N; pfam00081 907238002731 Iron/manganese superoxide dismutases, C-terminal domain; Region: Sod_Fe_C; pfam02777 907238002732 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238002733 S-adenosylmethionine binding site [chemical binding]; other site 907238002734 primosome assembly protein PriA; Validated; Region: PRK05580 907238002735 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238002736 ATP binding site [chemical binding]; other site 907238002737 putative Mg++ binding site [ion binding]; other site 907238002738 helicase superfamily c-terminal domain; Region: HELICc; smart00490 907238002739 Sporulation related domain; Region: SPOR; pfam05036 907238002740 Peptidase family M48; Region: Peptidase_M48; pfam01435 907238002741 HemK family putative methylases; Region: hemK_fam; TIGR00536 907238002742 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cl17173 907238002743 glutamate dehydrogenase; Provisional; Region: PRK09414 907238002744 Glu/Leu/Phe/Val dehydrogenase, dimerisation domain; Region: ELFV_dehydrog_N; pfam02812 907238002745 NAD(P) binding domain of glutamate dehydrogenase, subgroup 2; Region: NAD_bind_2_Glu_DH; cd05313 907238002746 NAD(P) binding site [chemical binding]; other site 907238002747 ResB protein required for cytochrome c biosynthesis [Posttranslational modification, protein turnover, chaperones]; Region: ResB; cl09125 907238002748 cytochrome c-type biogenesis protein CcsB; Region: cytochr_II_ccsB; TIGR03144 907238002749 SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide...; Region: SoxW; cd02951 907238002750 catalytic residues [active] 907238002751 ferrochelatase; Region: hemH; TIGR00109 907238002752 Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_N; cd03411 907238002753 C-terminal domain interface [polypeptide binding]; other site 907238002754 active site 907238002755 Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is...; Region: Ferrochelatase_C; cd00419 907238002756 active site 907238002757 N-terminal domain interface [polypeptide binding]; other site 907238002758 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1385 907238002759 RNA methyltransferase, RsmE family; Region: TIGR00046 907238002760 potential frameshift: common BLAST hit: gi|188527862|ref|YP_001910549.1| putative outer membrane protein 907238002761 Trimeric dUTP diphosphatases; Region: trimeric_dUTPase; cd07557 907238002762 trimer interface [polypeptide binding]; other site 907238002763 active site 907238002764 acetyl-CoA carboxylase, biotin carboxyl carrier protein; Region: BCCP; TIGR00531 907238002765 The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase; Region: biotinyl_domain; cd06850 907238002766 carboxyltransferase (CT) interaction site; other site 907238002767 biotinylation site [posttranslational modification]; other site 907238002768 biotin carboxylase; Validated; Region: PRK08462 907238002769 Carbamoyl-phosphate synthase L chain, N-terminal domain; Region: CPSase_L_chain; pfam00289 907238002770 Carbamoyl-phosphate synthase L chain, ATP binding domain; Region: CPSase_L_D2; pfam02786 907238002771 Biotin carboxylase C-terminal domain; Region: Biotin_carb_C; smart00878 907238002772 Methyltransferase domain; Region: Methyltransf_26; pfam13659 907238002773 Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]; Region: WecE; COG0399 907238002774 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary...; Region: AHBA_syn; cd00616 907238002775 inhibitor-cofactor binding pocket; inhibition site 907238002776 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238002777 catalytic residue [active] 907238002778 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain; Region: RNRR2; cd01049 907238002779 dimer interface [polypeptide binding]; other site 907238002780 putative radical transfer pathway; other site 907238002781 diiron center [ion binding]; other site 907238002782 tyrosyl radical; other site 907238002783 protein-L-isoaspartate(D-aspartate) O-methyltransferase; Region: pimt; TIGR00080 907238002784 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238002785 S-adenosylmethionine binding site [chemical binding]; other site 907238002786 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 907238002787 Predicted permeases [General function prediction only]; Region: COG0795 907238002788 tRNA pseudouridine(38-40) synthase; Region: hisT_truA; TIGR00071 907238002789 Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA; Region: PseudoU_synth_EcTruA; cd02570 907238002790 dimerization interface 3.5A [polypeptide binding]; other site 907238002791 active site 907238002792 UDP-glucose-4-epimerase GalE; Region: galE; TIGR01179 907238002793 UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs; Region: UDP_G4E_1_SDR_e; cd05247 907238002794 NAD binding site [chemical binding]; other site 907238002795 homodimer interface [polypeptide binding]; other site 907238002796 active site 907238002797 substrate binding site [chemical binding]; other site 907238002798 potential protein location (hypothetical protein HPIN_05400 [Helicobacter pylori India7]) that overlaps RNA (tRNA-I) 907238002799 classical (c) SDR, subgroup 5; Region: SDR_c5; cd05346 907238002800 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]; Region: COG4221 907238002801 putative NAD(P) binding site [chemical binding]; other site 907238002802 homodimer interface [polypeptide binding]; other site 907238002803 homotetramer interface [polypeptide binding]; other site 907238002804 active site 907238002805 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907238002806 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 907238002807 binding surface 907238002808 TPR motif; other site 907238002809 Sel1-like repeats; Region: SEL1; smart00671 907238002810 Sel1-like repeats; Region: SEL1; smart00671 907238002811 Sel1-like repeats; Region: SEL1; smart00671 907238002812 Entner-Doudoroff aldolase; Region: eda; TIGR01182 907238002813 KDPG and KHG aldolase; Region: KDPG_aldolase; cd00452 907238002814 active site 907238002815 intersubunit interface [polypeptide binding]; other site 907238002816 catalytic residue [active] 907238002817 phosphogluconate dehydratase; Validated; Region: PRK09054 907238002818 6-phosphogluconate dehydratase; Region: edd; TIGR01196 907238002819 Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]; Region: Zwf; COG0364 907238002820 Glucose-6-phosphate dehydrogenase, NAD binding domain; Region: G6PD_N; pfam00479 907238002821 Glucose-6-phosphate dehydrogenase, C-terminal domain; Region: G6PD_C; pfam02781 907238002822 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]; Region: NagB; COG0363 907238002823 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard...; Region: 6PGL; cd01400 907238002824 putative active site [active] 907238002825 glucokinase; Provisional; Region: glk; PRK00292 907238002826 glucokinase, proteobacterial type; Region: glk; TIGR00749 907238002827 Zn-dependent alcohol dehydrogenases [General function prediction only]; Region: AdhP; COG1064 907238002828 Cinnamyl alcohol dehydrogenases (CAD); Region: CAD1; cd05283 907238002829 putative NAD(P) binding site [chemical binding]; other site 907238002830 putative substrate binding site [chemical binding]; other site 907238002831 catalytic Zn binding site [ion binding]; other site 907238002832 structural Zn binding site [ion binding]; other site 907238002833 dimer interface [polypeptide binding]; other site 907238002834 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907238002835 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 907238002836 active site 907238002837 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002838 pyruvate flavodoxin oxidoreductase subunit gamma; Validated; Region: PRK05844 907238002839 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional; Region: PRK14029 907238002840 pyruvate flavodoxin oxidoreductase subunit delta; Reviewed; Region: porD; PRK09625 907238002841 4Fe-4S binding domain; Region: Fer4; pfam00037 907238002842 pyruvate flavodoxin oxidoreductase subunit alpha; Reviewed; Region: porA; PRK09622 907238002843 Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins; Region: TPP_PYR_PFOR_IOR-alpha_like; cd07034 907238002844 dimer interface [polypeptide binding]; other site 907238002845 PYR/PP interface [polypeptide binding]; other site 907238002846 TPP binding site [chemical binding]; other site 907238002847 substrate binding site [chemical binding]; other site 907238002848 Transketolase, C-terminal domain; Region: Transketolase_C; pfam02780 907238002849 pyruvate ferredoxin oxidoreductase subunit beta; Provisional; Region: PRK11865 907238002850 Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea...; Region: TPP_PFOR_porB_like; cd03376 907238002851 TPP-binding site [chemical binding]; other site 907238002852 putative dimer interface [polypeptide binding]; other site 907238002853 adenylosuccinate lyase; Provisional; Region: PRK08470 907238002854 Adenylsuccinate lyase (ASL)_subgroup 1; Region: Adenylsuccinate_lyase_1; cd01360 907238002855 tetramer interface [polypeptide binding]; other site 907238002856 active site 907238002857 Adenylosuccinate lyase C-terminus; Region: ADSL_C; smart00998 907238002858 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002859 excinuclease ABC subunit B; Provisional; Region: PRK05298 907238002860 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238002861 ATP binding site [chemical binding]; other site 907238002862 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 907238002863 putative Mg++ binding site [ion binding]; other site 907238002864 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 907238002865 nucleotide binding region [chemical binding]; other site 907238002866 ATP-binding site [chemical binding]; other site 907238002867 Ultra-violet resistance protein B; Region: UvrB; pfam12344 907238002868 UvrB/uvrC motif; Region: UVR; pfam02151 907238002869 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238002870 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 907238002871 binding surface 907238002872 FOG: TPR repeat, SEL1 subfamily [General function prediction only]; Region: COG0790 907238002873 TPR motif; other site 907238002874 Sel1-like repeats; Region: SEL1; smart00671 907238002875 Sel1-like repeats; Region: SEL1; smart00671 907238002876 Sel1-like repeats; Region: SEL1; smart00671 907238002877 Gamma-glutamyltransferase [Amino acid transport and metabolism]; Region: Ggt; COG0405 907238002878 gamma-glutamyltranspeptidase; Region: g_glut_trans; TIGR00066 907238002879 flagellar hook-associated protein FlgK; Validated; Region: flgK; PRK08471 907238002880 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907238002881 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 907238002882 DNA-methyltransferase (dcm); Region: dcm; TIGR00675 907238002883 cofactor binding site; other site 907238002884 DNA binding site [nucleotide binding] 907238002885 substrate interaction site [chemical binding]; other site 907238002886 Anti-sigma-28 factor, FlgM; Region: FlgM; cl01052 907238002887 FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]; Region: SlpA; COG1047 907238002888 FKBP-type peptidyl-prolyl cis-trans isomerase; Region: FKBP_C; pfam00254 907238002889 tol-pal system protein YbgF; Region: tol_pal_ybgF; TIGR02795 907238002890 Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]; Region: OmpA; COG2885 907238002891 Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA; Region: OmpA_C-like; cd07185 907238002892 ligand binding site [chemical binding]; other site 907238002893 translocation protein TolB; Provisional; Region: tolB; PRK04043 907238002894 TolB amino-terminal domain; Region: TolB_N; pfam04052 907238002895 WD40-like Beta Propeller Repeat; Region: PD40; pfam07676 907238002896 TonB C terminal; Region: TonB_2; pfam13103 907238002897 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 907238002898 TolR protein; Region: tolR; TIGR02801 907238002899 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 907238002900 ATP synthase, F1 epsilon subunit (delta in mitochondria); Region: ATP_synt_epsi; TIGR01216 907238002901 mitochondrial ATP synthase delta subunit; Region: F1-ATPase_delta; cd12152 907238002902 gamma subunit interface [polypeptide binding]; other site 907238002903 epsilon subunit interface [polypeptide binding]; other site 907238002904 LBP interface [polypeptide binding]; other site 907238002905 F0F1 ATP synthase subunit beta; Validated; Region: PRK09280 907238002906 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 907238002907 F1 ATP synthase beta subunit, nucleotide-binding domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a...; Region: F1-ATPase_beta; cd01133 907238002908 alpha subunit interaction interface [polypeptide binding]; other site 907238002909 Walker A motif; other site 907238002910 ATP binding site [chemical binding]; other site 907238002911 Walker B motif; other site 907238002912 inhibitor binding site; inhibition site 907238002913 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 907238002914 mitochondrial ATP synthase gamma subunit; Region: F1-ATPase_gamma; cd12151 907238002915 core domain interface [polypeptide binding]; other site 907238002916 delta subunit interface [polypeptide binding]; other site 907238002917 epsilon subunit interface [polypeptide binding]; other site 907238002918 F0F1 ATP synthase subunit alpha; Validated; Region: PRK09281 907238002919 ATP synthase alpha/beta family, beta-barrel domain; Region: ATP-synt_ab_N; pfam02874 907238002920 F1 ATP synthase alpha, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to...; Region: F1_ATPase_alpha; cd01132 907238002921 beta subunit interaction interface [polypeptide binding]; other site 907238002922 Walker A motif; other site 907238002923 ATP binding site [chemical binding]; other site 907238002924 Walker B motif; other site 907238002925 ATP synthase alpha/beta chain, C terminal domain; Region: ATP-synt_ab_C; pfam00306 907238002926 F0F1 ATP synthase subunit delta; Provisional; Region: PRK13431 907238002927 F0F1 ATP synthase subunit B; Validated; Region: PRK08475 907238002928 F0F1 ATP synthase subunit B'; Validated; Region: PRK08476 907238002929 F0F1-type ATP synthase, subunit b [Energy production and conversion]; Region: AtpF; COG0711 907238002930 ParB/RepB/Spo0J family partition protein; Region: parB_part; TIGR00180 907238002931 ParB-like nuclease domain; Region: ParB; smart00470 907238002932 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 907238002933 ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the...; Region: ParA; cd02042 907238002934 P-loop; other site 907238002935 Magnesium ion binding site [ion binding]; other site 907238002936 biotin--protein ligase; Provisional; Region: PRK08477 907238002937 Biotin/lipoate A/B protein ligase family; Region: BPL_LplA_LipB; pfam03099 907238002938 methionyl-tRNA formyltransferase; Reviewed; Region: fmt; PRK00005 907238002939 Methionyl-tRNA formyltransferase, N-terminal hydrolase domain; Region: FMT_core_Met-tRNA-FMT_N; cd08646 907238002940 putative active site [active] 907238002941 substrate binding site [chemical binding]; other site 907238002942 putative cosubstrate binding site; other site 907238002943 catalytic site [active] 907238002944 Formyl transferase, C-terminal domain; Region: Formyl_trans_C; pfam02911 907238002945 potential frameshift: common BLAST hit: gi|210135301|ref|YP_002301740.1| ATPase 907238002946 potential frameshift: common BLAST hit: gi|308184882|ref|YP_003929015.1| ATPase 907238002947 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4487 907238002948 Uncharacterized protein conserved in bacteria (DUF2130); Region: DUF2130; pfam09903 907238002949 50S ribosomal protein L19; Provisional; Region: rplS; PRK05338 907238002950 tRNA (Guanine-1)-methyltransferase; Region: tRNA_m1G_MT; cl00407 907238002951 16S rRNA-processing protein RimM; Provisional; Region: rimM; PRK14593 907238002952 RimM N-terminal domain; Region: RimM; pfam01782 907238002953 PRC-barrel domain; Region: PRC; pfam05239 907238002954 Predicted RNA-binding protein (contains KH domain) [General function prediction only]; Region: COG1837 907238002955 KH domain; Region: KH_4; pfam13083 907238002956 G-X-X-G motif; other site 907238002957 30S ribosomal protein S16; Reviewed; Region: rpsP; PRK00040 907238002958 signal recognition particle protein; Provisional; Region: PRK10867 907238002959 SRP54-type protein, helical bundle domain; Region: SRP54_N; smart00963 907238002960 The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The...; Region: SRP; cd03115 907238002961 P loop; other site 907238002962 GTP binding site [chemical binding]; other site 907238002963 Signal peptide binding domain; Region: SRP_SPB; pfam02978 907238002964 valyl-tRNA synthetase; Reviewed; Region: valS; PRK05729 907238002965 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 907238002966 active site 907238002967 HIGH motif; other site 907238002968 nucleotide binding site [chemical binding]; other site 907238002969 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 907238002970 catalytic core domain of valyl-tRNA synthetases; Region: ValRS_core; cd00817 907238002971 active site 907238002972 KMSKS motif; other site 907238002973 Anticodon-binding domain of valyl tRNA synthetases; Region: Anticodon_Ia_Val; cd07962 907238002974 anticodon binding site; other site 907238002975 flagellar assembly protein FliW; Provisional; Region: PRK13283 907238002976 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Region: murG; TIGR01133 907238002977 MurG is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide...; Region: GT1_MurG; cd03785 907238002978 active site 907238002979 homodimer interface [polypeptide binding]; other site 907238002980 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002981 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238002982 pyrroline-5-carboxylate reductase; Reviewed; Region: PRK11880 907238002983 NADP oxidoreductase coenzyme F420-dependent; Region: F420_oxidored; cl17232 907238002984 Protein involved in cell division [Cell division and chromosome partitioning]; Region: Fic; COG2184 907238002985 Fic/DOC family; Region: Fic; cl00960 907238002986 metal-binding heat shock protein; Provisional; Region: PRK00016 907238002987 flavodoxin FldA; Validated; Region: PRK09267 907238002988 Uncharacterized membrane-associated protein [Function unknown]; Region: DedA; COG0586 907238002989 SNARE associated Golgi protein; Region: SNARE_assoc; pfam09335 907238002990 Uncharacterized protein, possibly involved in nitrogen fixation [Inorganic ion transport and metabolism]; Region: FixS; COG3197 907238002991 Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]; Region: TrxB; COG0492 907238002992 NAD(P)-binding Rossmann-like domain; Region: NAD_binding_8; cl17500 907238002993 Pyridine nucleotide-disulphide oxidoreductase; Region: Pyr_redox; pfam00070 907238002994 Major Facilitator Superfamily; Region: MFS_1; pfam07690 907238002995 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 907238002996 glucose-6-phosphate isomerase; Reviewed; Region: pgi; PRK00179 907238002997 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_1; cd05015 907238002998 active site 907238002999 dimer interface [polypeptide binding]; other site 907238003000 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of...; Region: SIS_PGI_2; cd05016 907238003001 dimer interface [polypeptide binding]; other site 907238003002 active site 907238003003 Putative outer membrane protein; Region: HP_OMP_2; pfam02521 907238003004 carbon starvation protein A; Provisional; Region: PRK15015 907238003005 Carbon starvation protein CstA; Region: CstA; pfam02554 907238003006 C-terminal domain on CstA (DUF4161); Region: DUF4161; pfam13722 907238003007 ABC-type arginine transport system, permease component [Amino acid transport and metabolism]; Region: ArtQ; COG4215 907238003008 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238003009 dimer interface [polypeptide binding]; other site 907238003010 conserved gate region; other site 907238003011 putative PBP binding loops; other site 907238003012 ABC-ATPase subunit interface; other site 907238003013 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238003014 dimer interface [polypeptide binding]; other site 907238003015 conserved gate region; other site 907238003016 putative PBP binding loops; other site 907238003017 ABC-ATPase subunit interface; other site 907238003018 ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]; Region: GlnQ; COG1126 907238003019 ATP-binding cassette domain of the histidine and glutamine transporters; Region: ABC_HisP_GlnQ; cd03262 907238003020 Walker A/P-loop; other site 907238003021 ATP binding site [chemical binding]; other site 907238003022 Q-loop/lid; other site 907238003023 ABC transporter signature motif; other site 907238003024 Walker B; other site 907238003025 D-loop; other site 907238003026 H-loop/switch region; other site 907238003027 Bacterial periplasmic substrate-binding proteins; Region: PBPb; smart00062 907238003028 Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic...; Region: PBPb; cd00134 907238003029 substrate binding pocket [chemical binding]; other site 907238003030 membrane-bound complex binding site; other site 907238003031 hinge residues; other site 907238003032 Fucose permease [Carbohydrate transport and metabolism]; Region: FucP; COG0738 907238003033 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 907238003034 putative substrate translocation pore; other site 907238003035 Xanthine/uracil/vitamin C permease [Nucleotide transport and metabolism]; Region: COG2252 907238003036 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238003037 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238003038 S-adenosylmethionine binding site [chemical binding]; other site 907238003039 GIY-YIG nuclease domain superfamily; Region: GIY-YIG_SF; cl15257 907238003040 GIY-YIG motif/motif A; other site 907238003041 active site 907238003042 catalytic site [active] 907238003043 metal binding site [ion binding]; metal-binding site 907238003044 purine-nucleoside phosphorylase, family 1 (deoD); Region: deoD; TIGR00107 907238003045 phosphopentomutase; Provisional; Region: PRK05362 907238003046 Metalloenzyme superfamily; Region: Metalloenzyme; pfam01676 907238003047 Nucleoside permease [Nucleotide transport and metabolism]; Region: NupC; COG1972 907238003048 Na+ dependent nucleoside transporter N-terminus; Region: Nucleos_tra2_N; pfam01773 907238003049 Nucleoside recognition; Region: Gate; pfam07670 907238003050 Na+ dependent nucleoside transporter C-terminus; Region: Nucleos_tra2_C; pfam07662 907238003051 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 907238003052 Major Facilitator Superfamily; Region: MFS_1; pfam07690 907238003053 putative substrate translocation pore; other site 907238003054 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional; Region: PRK10696 907238003055 This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which binds to Adenosine group. This subfamily; Region: Alpha_ANH_like_II; cd01993 907238003056 Ligand Binding Site [chemical binding]; other site 907238003057 Kef-type K+ transport systems, membrane components [Inorganic ion transport and metabolism]; Region: KefB; COG0475 907238003058 Sodium/hydrogen exchanger family; Region: Na_H_Exchanger; pfam00999 907238003059 Na+-driven multidrug efflux pump [Defense mechanisms]; Region: NorM; COG0534 907238003060 Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA; Region: MATE_MepA_like; cd13143 907238003061 putative arabinose transporter; Provisional; Region: PRK03545 907238003062 The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of...; Region: MFS; cd06174 907238003063 putative substrate translocation pore; other site 907238003064 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907238003065 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 907238003066 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907238003067 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 907238003068 antiporter inner membrane protein; Provisional; Region: PRK11670 907238003069 Domain of unknown function DUF59; Region: DUF59; cl00941 907238003070 MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions...; Region: MRP-like; cd02037 907238003071 3-oxoacyl-(acyl-carrier-protein) synthase III; Region: fabH; TIGR00747 907238003072 Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl...; Region: KAS_III; cd00830 907238003073 dimer interface [polypeptide binding]; other site 907238003074 active site 907238003075 CoA binding pocket [chemical binding]; other site 907238003076 fatty acid/phospholipid synthesis protein PlsX; Region: plsX; TIGR00182 907238003077 Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]; Region: RpmF; COG0333 907238003078 Uncharacterized ACR, COG1399; Region: DUF177; cl00616 907238003079 Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside...; Region: NDPk_I; cd04413 907238003080 active site 907238003081 multimer interface [polypeptide binding]; other site 907238003082 S-adenosylmethionine synthetase; Validated; Region: PRK05250 907238003083 S-adenosylmethionine synthetase, N-terminal domain; Region: S-AdoMet_synt_N; pfam00438 907238003084 S-adenosylmethionine synthetase, central domain; Region: S-AdoMet_synt_M; pfam02772 907238003085 S-adenosylmethionine synthetase, C-terminal domain; Region: S-AdoMet_synt_C; pfam02773 907238003086 Site-specific recombinase XerD [DNA replication, recombination, and repair]; Region: XerD; COG4974 907238003087 phiLC3 phage and phage-related integrases, site-specific recombinases, DNA breaking-rejoining enzymes, C-terminal catalytic domain. This CD includes various bacterial (mainly gram positive) and phage integrases, including those similar to Lactococcus...; Region: INT_phiLC3_C; cd01189 907238003088 Int/Topo IB signature motif; other site 907238003089 Sugar-specific transcriptional regulator TrmB; Region: TrmB; cl17775 907238003090 Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to...; Region: HTH_ARSR; cl17220 907238003091 putative DNA binding site [nucleotide binding]; other site 907238003092 putative Zn2+ binding site [ion binding]; other site 907238003093 RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H+ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and...; Region: RecA-like_NTPases; cl17233 907238003094 Walker A motif; other site 907238003095 ATP binding site [chemical binding]; other site 907238003096 CHC2 zinc finger; Region: zf-CHC2; pfam01807 907238003097 DNA primase catalytic core, N-terminal domain; Region: Toprim_N; pfam08275 907238003098 Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from...; Region: TOPRIM; cl00718 907238003099 active site 907238003100 metal binding site [ion binding]; metal-binding site 907238003101 Chromosome segregation ATPases [Cell division and chromosome partitioning]; Region: Smc; COG1196 907238003102 phosphodiesterase; Provisional; Region: PRK12704 907238003103 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238003104 Protein of unknown function (DUF3519); Region: DUF3519; pfam12033 907238003105 Protein of unknown function (DUF4043); Region: DUF4043; pfam13252 907238003106 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG5410 907238003107 DEAD-like helicases superfamily; Region: DEXDc; smart00487 907238003108 DNA primase; Validated; Region: dnaG; PRK05667 907238003109 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Region: lipid_A_lpxD; TIGR01853 907238003110 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD; Region: LpxD; pfam04613 907238003111 UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2; Region: LbH_LpxD; cd03352 907238003112 trimer interface [polypeptide binding]; other site 907238003113 active site 907238003114 UDP-GlcNAc binding site [chemical binding]; other site 907238003115 lipid binding site [chemical binding]; lipid-binding site 907238003116 enoyl-(acyl carrier protein) reductase; Provisional; Region: PRK08415 907238003117 Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR; Region: ENR_SDR; cd05372 907238003118 NAD binding site [chemical binding]; other site 907238003119 homotetramer interface [polypeptide binding]; other site 907238003120 homodimer interface [polypeptide binding]; other site 907238003121 substrate binding site [chemical binding]; other site 907238003122 active site 907238003123 triosephosphate isomerase; Provisional; Region: PRK14567 907238003124 Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually...; Region: TIM; cd00311 907238003125 substrate binding site [chemical binding]; other site 907238003126 dimer interface [polypeptide binding]; other site 907238003127 catalytic triad [active] 907238003128 fumarate reductase cytochrome b-556 subunit; Provisional; Region: PRK13553 907238003129 Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone...; Region: QFR_TypeB_TM; cd00581 907238003130 Iron-sulfur protein interface; other site 907238003131 proximal heme binding site [chemical binding]; other site 907238003132 distal heme binding site [chemical binding]; other site 907238003133 dimer interface [polypeptide binding]; other site 907238003134 fumarate reductase flavoprotein subunit; Provisional; Region: PRK08626 907238003135 L-aspartate oxidase; Provisional; Region: PRK06175 907238003136 Fumarate reductase flavoprotein C-term; Region: Succ_DH_flav_C; pfam02910 907238003137 fumarate reductase iron-sulfur subunit; Provisional; Region: frdB; PRK13552 907238003138 2Fe-2S iron-sulfur cluster binding domain; Region: Fer2_3; pfam13085 907238003139 The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved...; Region: HCP_like; cl14655 907238003140 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_1; cd09111 907238003141 PLD-like domain; Region: PLDc_2; pfam13091 907238003142 putative active site [active] 907238003143 catalytic site [active] 907238003144 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins; Region: PLDc_ymdC_like_2; cd09113 907238003145 PLD-like domain; Region: PLDc_2; pfam13091 907238003146 putative active site [active] 907238003147 catalytic site [active] 907238003148 Uncharacterized protein family, UPF0114; Region: UPF0114; cl01078 907238003149 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238003150 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907238003151 AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis...; Region: AE_Prim_S_like; cd00525 907238003152 nucleotide binding site [chemical binding]; other site 907238003153 serine hydroxymethyltransferase; Reviewed; Region: PRK13034 907238003154 Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl...; Region: SHMT; cd00378 907238003155 dimer interface [polypeptide binding]; other site 907238003156 active site 907238003157 glycine-pyridoxal phosphate binding site [chemical binding]; other site 907238003158 folate binding site [chemical binding]; other site 907238003159 lysyl-tRNA synthetase; Reviewed; Region: lysS; PRK00484 907238003160 LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop; Region: LysRS_N; cd04322 907238003161 dimer interface [polypeptide binding]; other site 907238003162 putative anticodon binding site; other site 907238003163 Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three...; Region: LysRS_core; cd00775 907238003164 motif 1; other site 907238003165 active site 907238003166 motif 2; other site 907238003167 motif 3; other site 907238003168 Uncharacterized membrane protein, required for colicin V production [General function prediction only]; Region: CvpA; COG1286 907238003169 Colicin V production protein; Region: Colicin_V; pfam02674 907238003170 Fungal protein of unknown function (DUF1742); Region: DUF1742; pfam08432 907238003171 apolipoprotein N-acyltransferase; Reviewed; Region: PRK12291 907238003172 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cl11424 907238003173 active site 907238003174 catalytic triad [active] 907238003175 ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]; Region: SalX; COG1136 907238003176 ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein; Region: ABC_MJ0796_LolCDE_FtsE; cd03255 907238003177 Walker A/P-loop; other site 907238003178 ATP binding site [chemical binding]; other site 907238003179 Q-loop/lid; other site 907238003180 ABC transporter signature motif; other site 907238003181 Walker B; other site 907238003182 D-loop; other site 907238003183 H-loop/switch region; other site 907238003184 pseudaminic acid synthase; Region: PseI; TIGR03586 907238003185 NeuB family; Region: NeuB; pfam03102 907238003186 C-terminal SAF domain of sialic acid synthetase; Region: SAF_NeuB_like; cd11615 907238003187 NeuB binding interface [polypeptide binding]; other site 907238003188 putative substrate binding site [chemical binding]; other site 907238003189 Carbonic anhydrase [Inorganic ion transport and metabolism]; Region: Cah; COG3338 907238003190 Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon...; Region: alpha_CA_prokaryotic_like; cd03124 907238003191 active site 907238003192 zinc binding site [ion binding]; other site 907238003193 Helicobacter pylori protein of unknown function (DUF874); Region: DUF874; pfam05917 907238003194 aspartate-semialdehyde dehydrogenase (peptidoglycan organisms); Region: asd_B; TIGR01296 907238003195 Semialdehyde dehydrogenase, NAD binding domain; Region: Semialdhyde_dh; smart00859 907238003196 Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]; Region: HisS; COG0124 907238003197 Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for...; Region: HisRS-like_core; cd00773 907238003198 dimer interface [polypeptide binding]; other site 907238003199 motif 1; other site 907238003200 active site 907238003201 motif 2; other site 907238003202 motif 3; other site 907238003203 HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is...; Region: HisRS_anticodon; cd00859 907238003204 anticodon binding site; other site 907238003205 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907238003206 Lipopolysaccharide heptosyltransferase is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from...; Region: GT1_LPS_heptosyltransferase; cd03789 907238003207 putative active site [active] 907238003208 elongation factor G; Reviewed; Region: PRK00007 907238003209 Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis; Region: EF-G; cd01886 907238003210 G1 box; other site 907238003211 putative GEF interaction site [polypeptide binding]; other site 907238003212 GTP/Mg2+ binding site [chemical binding]; other site 907238003213 Switch I region; other site 907238003214 G2 box; other site 907238003215 G3 box; other site 907238003216 Switch II region; other site 907238003217 G4 box; other site 907238003218 G5 box; other site 907238003219 EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis...; Region: EFG_mtEFG_II; cd04088 907238003220 EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2...; Region: EFG_mtEFG1_IV; cd01434 907238003221 EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2...; Region: EFG_mtEFG_C; cd03713 907238003222 30S ribosomal protein S7; Validated; Region: PRK05302 907238003223 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit...; Region: Ribosomal_S12; cd03368 907238003224 S17 interaction site [polypeptide binding]; other site 907238003225 S8 interaction site; other site 907238003226 16S rRNA interaction site [nucleotide binding]; other site 907238003227 streptomycin interaction site [chemical binding]; other site 907238003228 23S rRNA interaction site [nucleotide binding]; other site 907238003229 aminoacyl-tRNA interaction site (A-site) [nucleotide binding]; other site 907238003230 bifunctional DNA-directed RNA polymerase subunit beta/beta'; Reviewed; Region: PRK09603 907238003231 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cl17585 907238003232 RNA polymerase Rpb2, domain 2; Region: RNA_pol_Rpb2_2; pfam04561 907238003233 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 907238003234 RPB11 interaction site [polypeptide binding]; other site 907238003235 RPB12 interaction site [polypeptide binding]; other site 907238003236 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase...; Region: RNA_pol_B_RPB2; cd00653 907238003237 RPB3 interaction site [polypeptide binding]; other site 907238003238 RPB1 interaction site [polypeptide binding]; other site 907238003239 RPB11 interaction site [polypeptide binding]; other site 907238003240 RPB10 interaction site [polypeptide binding]; other site 907238003241 RNA polymerase Rpb1, domain 1; Region: RNA_pol_Rpb1_1; pfam04997 907238003242 RNA polymerase I subunit A N-terminus; Region: RPOLA_N; smart00663 907238003243 RNA polymerase Rpb1, domain 3; Region: RNA_pol_Rpb1_3; pfam04983 907238003244 RNA polymerase Rpb1, domain 4; Region: RNA_pol_Rpb1_4; pfam05000 907238003245 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 907238003246 Rpb1 - Rpb6 interaction site [polypeptide binding]; other site 907238003247 Largest subunit of RNA polymerase (RNAP), C-terminal domain; Region: RNAP_largest_subunit_C; cl11429 907238003248 Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Region: RNAP_beta'_C; cd02655 907238003249 DNA binding site [nucleotide binding] 907238003250 Rpb1 (beta') - Rpb2 (beta) interaction site [polypeptide binding]; other site 907238003251 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of...; Region: Ribosomal_L7_L12; cd00387 907238003252 core dimer interface [polypeptide binding]; other site 907238003253 peripheral dimer interface [polypeptide binding]; other site 907238003254 L10 interface [polypeptide binding]; other site 907238003255 L11 interface [polypeptide binding]; other site 907238003256 putative EF-Tu interaction site [polypeptide binding]; other site 907238003257 putative EF-G interaction site [polypeptide binding]; other site 907238003258 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein...; Region: Ribosomal_L10; cd05797 907238003259 23S rRNA interface [nucleotide binding]; other site 907238003260 Interface with L7/L12 ribosomal proteins [polypeptide binding]; other site 907238003261 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds...; Region: Ribosomal_L1; cd00403 907238003262 mRNA/rRNA interface [nucleotide binding]; other site 907238003263 50S ribosomal protein L11; Validated; Region: rplK; PRK00140 907238003264 Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal...; Region: Ribosomal_L11; cd00349 907238003265 23S rRNA interface [nucleotide binding]; other site 907238003266 L7/L12 interface [polypeptide binding]; other site 907238003267 putative thiostrepton binding site; other site 907238003268 L25 interface [polypeptide binding]; other site 907238003269 transcription antitermination protein NusG; Validated; Region: nusG; PRK05609 907238003270 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1; Region: NGN_Bact_1; cd09891 907238003271 putative homodimer interface [polypeptide binding]; other site 907238003272 NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus; Region: KOW_NusG; cd06091 907238003273 heterodimer interface [polypeptide binding]; other site 907238003274 homodimer interface [polypeptide binding]; other site 907238003275 SecE/Sec61-gamma subunits of protein translocation complex; Region: SecE; cl00481 907238003276 potential protein location (hypothetical protein HPIN_06345 [Helicobacter pylori India7]) that overlaps RNA (tRNA-W) 907238003277 50S ribosomal protein L33; Validated; Region: rpmG; PRK00595 907238003278 elongation factor Tu; Reviewed; Region: PRK00049 907238003279 Elongation Factor Tu (EF-Tu) GTP-binding proteins; Region: EF_Tu; cd01884 907238003280 G1 box; other site 907238003281 GEF interaction site [polypeptide binding]; other site 907238003282 GTP/Mg2+ binding site [chemical binding]; other site 907238003283 Switch I region; other site 907238003284 G2 box; other site 907238003285 G3 box; other site 907238003286 Switch II region; other site 907238003287 G4 box; other site 907238003288 G5 box; other site 907238003289 EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the...; Region: EFTU_II; cd03697 907238003290 Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts); Region: EFTU_III; cd03707 907238003291 Antibiotic Binding Site [chemical binding]; other site 907238003292 ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]; Region: MdlB; COG1132 907238003293 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238003294 Walker A/P-loop; other site 907238003295 ATP binding site [chemical binding]; other site 907238003296 Q-loop/lid; other site 907238003297 ABC transporter signature motif; other site 907238003298 Walker B; other site 907238003299 D-loop; other site 907238003300 H-loop/switch region; other site 907238003301 haloacid dehalogenase-like hydrolase; Region: Hydrolase; pfam00702 907238003302 HAD-hyrolase-like; Region: Hydrolase_like; pfam13242 907238003303 Adenine-specific DNA methylase [DNA replication, recombination, and repair]; Region: COG3392 907238003304 D12 class N6 adenine-specific DNA methyltransferase; Region: MethyltransfD12; pfam02086 907238003305 Helicobacter pylori IceA2 protein; Region: IceA2; pfam05862 907238003306 serine O-acetyltransferase; Region: cysE; TIGR01172 907238003307 Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of...; Region: LbH_SAT; cd03354 907238003308 trimer interface [polypeptide binding]; other site 907238003309 active site 907238003310 substrate binding site [chemical binding]; other site 907238003311 CoA binding site [chemical binding]; other site 907238003312 F0F1 ATP synthase subunit C; Validated; Region: PRK08482 907238003313 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 907238003314 polynucleotide phosphorylase/polyadenylase; Provisional; Region: PRK11824 907238003315 oligomer interface [polypeptide binding]; other site 907238003316 RNA binding site [nucleotide binding]; other site 907238003317 Polyribonucleotide nucleotidyltransferase, RNA binding domain; Region: PNPase; pfam03726 907238003318 RNase PH-like 3'-5' exoribonucleases; Region: RNase_PH; cl03114 907238003319 oligomer interface [polypeptide binding]; other site 907238003320 RNA binding site [nucleotide binding]; other site 907238003321 Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to...; Region: PNPase_KH; cd02393 907238003322 putative nucleic acid binding region [nucleotide binding]; other site 907238003323 G-X-X-G motif; other site 907238003324 Ribosomal protein S1-like RNA-binding domain; Region: S1; smart00316 907238003325 RNA binding site [nucleotide binding]; other site 907238003326 Predicted phosphoribosyltransferases [General function prediction only]; Region: COG1926 907238003327 Organic solvent tolerance protein OstA [Cell envelope biogenesis, outer membrane]; Region: Imp; COG1452 907238003328 Organic solvent tolerance protein; Region: OstA_C; pfam04453 907238003329 Predicted membrane protein/domain [Function unknown]; Region: COG1714 907238003330 phosphoribosylamine--glycine ligase; Region: purD; TIGR00877 907238003331 Phosphoribosylglycinamide synthetase, N domain; Region: GARS_N; pfam02844 907238003332 Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; Region: GARS_A; pfam01071 907238003333 Phosphoribosylglycinamide synthetase, C domain; Region: GARS_C; pfam02843 907238003334 ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]; Region: ZnuC; COG1121 907238003335 ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; Region: ABC_DR_subfamily_A; cd03230 907238003336 Walker A/P-loop; other site 907238003337 ATP binding site [chemical binding]; other site 907238003338 Q-loop/lid; other site 907238003339 ABC transporter signature motif; other site 907238003340 Walker B; other site 907238003341 D-loop; other site 907238003342 H-loop/switch region; other site 907238003343 Undecaprenyl pyrophosphate synthase [Lipid metabolism]; Region: UppS; COG0020 907238003344 Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl...; Region: CIS_IPPS; cd00475 907238003345 catalytic residue [active] 907238003346 putative FPP diphosphate binding site; other site 907238003347 putative FPP binding hydrophobic cleft; other site 907238003348 dimer interface [polypeptide binding]; other site 907238003349 putative IPP diphosphate binding site; other site 907238003350 FAD/FMN-containing dehydrogenases [Energy production and conversion]; Region: GlcD; COG0277 907238003351 FAD binding domain; Region: FAD_binding_4; pfam01565 907238003352 Fe-S oxidoreductase [Energy production and conversion]; Region: GlpC; COG0247 907238003353 Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins...; Region: RHOD; cd00158 907238003354 active site residue [active] 907238003355 uroporphyrinogen-III synthase; Reviewed; Region: hemD; PRK05928 907238003356 Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in...; Region: HemD; cd06578 907238003357 active site 907238003358 camphor resistance protein CrcB; Provisional; Region: PRK14204 907238003359 coproporphyrinogen III oxidase; Provisional; Region: PRK08446 907238003360 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238003361 FeS/SAM binding site; other site 907238003362 HemN C-terminal domain; Region: HemN_C; pfam06969 907238003363 Cytochrome c553 [Energy production and conversion]; Region: COG2863 907238003364 Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the Nudix hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant...; Region: Ap4A_hydrolase_plant_like; cd03671 907238003365 putative active site [active] 907238003366 Ap4A binding site [chemical binding]; other site 907238003367 nudix motif; other site 907238003368 putative metal binding site [ion binding]; other site 907238003369 aspartate kinase; Reviewed; Region: PRK06635 907238003370 AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive...; Region: AAK_AKii-LysC-BS; cd04261 907238003371 putative nucleotide binding site [chemical binding]; other site 907238003372 putative catalytic residues [active] 907238003373 putative Mg ion binding site [ion binding]; other site 907238003374 putative aspartate binding site [chemical binding]; other site 907238003375 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins; Region: ACT_AKii-LysC-BS-like_1; cd04913 907238003376 putative allosteric regulatory site; other site 907238003377 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains; Region: ACT_AKii-LysC-BS-like_2; cd04936 907238003378 putative allosteric regulatory residue; other site 907238003379 DNA replication regulator; Region: HobA; pfam12163 907238003380 DNA polymerase III subunit delta'; Validated; Region: PRK08485 907238003381 DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and...; Region: DHPS; cd00739 907238003382 dihydropteroate synthase; Region: DHPS; TIGR01496 907238003383 substrate binding pocket [chemical binding]; other site 907238003384 dimer interface [polypeptide binding]; other site 907238003385 inhibitor binding site; inhibition site 907238003386 Permeases of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism / Amino acid transport and metabolism / General function prediction only]; Region: RhaT; COG0697 907238003387 EamA-like transporter family; Region: EamA; pfam00892 907238003388 Dolichyl-phosphate-mannose-protein mannosyltransferase; Region: PMT_2; cl17364 907238003389 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2952 907238003390 Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]; Region: CarA; COG0505 907238003391 Carbamoyl-phosphate synthase small chain, CPSase domain; Region: CPSase_sm_chain; pfam00988 907238003392 Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II; Region: GATase1_CPSase; cd01744 907238003393 catalytic site [active] 907238003394 subunit interface [polypeptide binding]; other site 907238003395 formamidase; Provisional; Region: amiF; PRK13287 907238003396 aliphatic amidases (class 2 nitrilases); Region: aliphatic_amidase; cd07565 907238003397 multimer interface [polypeptide binding]; other site 907238003398 active site 907238003399 catalytic triad [active] 907238003400 dimer interface [polypeptide binding]; other site 907238003401 Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard...; Region: Maf_Ham1; cl00276 907238003402 putative active site [active] 907238003403 alanyl-tRNA synthetase; Reviewed; Region: alaS; PRK00252 907238003404 Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent...; Region: AlaRS_core; cd00673 907238003405 motif 1; other site 907238003406 active site 907238003407 motif 2; other site 907238003408 motif 3; other site 907238003409 Threonyl and Alanyl tRNA synthetase second additional domain; Region: tRNA_SAD; smart00863 907238003410 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG2841 907238003411 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238003412 30S ribosomal protein S18; Reviewed; Region: rpsR; PRK00391 907238003413 Single-stranded DNA-binding protein [DNA replication, recombination, and repair]; Region: Ssb; COG0629 907238003414 SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date...; Region: SSB_OBF; cd04496 907238003415 dimer interface [polypeptide binding]; other site 907238003416 ssDNA binding site [nucleotide binding]; other site 907238003417 tetramer (dimer of dimers) interface [polypeptide binding]; other site 907238003418 30S ribosomal protein S6; Reviewed; Region: rpsF; PRK00453 907238003419 DNA polymerase III subunit delta; Validated; Region: PRK08487 907238003420 DNA polymerase III, delta subunit; Region: DNA_pol3_delta; pfam06144 907238003421 Exoribonuclease R [Transcription]; Region: VacB; COG0557 907238003422 RNB domain; Region: RNB; pfam00773 907238003423 shikimate 5-dehydrogenase; Region: aroE; TIGR00507 907238003424 Shikimate dehydrogenase substrate binding domain; Region: Shikimate_dh_N; pfam08501 907238003425 NAD(P) binding domain of Shikimate dehydrogenase; Region: NAD_bind_Shikimate_DH; cd01065 907238003426 shikimate binding site; other site 907238003427 NAD(P) binding site [chemical binding]; other site 907238003428 Bacterial SH3 domain; Region: SH3_3; pfam08239 907238003429 ABC-type uncharacterized transport system, permease component [General function prediction only]; Region: COG4174 907238003430 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and...; Region: TM_PBP2; cd06261 907238003431 dimer interface [polypeptide binding]; other site 907238003432 conserved gate region; other site 907238003433 putative PBP binding loops; other site 907238003434 ABC-ATPase subunit interface; other site 907238003435 ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]; Region: OppA; COG4166 907238003436 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold; Region: PBP2_NikA_DppA_OppA_like_14; cd08497 907238003437 tryptophanyl-tRNA synthetase II; Reviewed; Region: PRK12282 907238003438 catalytic core domain of tryptophanyl-tRNA synthetase; Region: TrpRS_core; cd00806 907238003439 active site 907238003440 HIGH motif; other site 907238003441 dimer interface [polypeptide binding]; other site 907238003442 KMSKS motif; other site 907238003443 biotin biosynthesis protein BioC; Region: BioC; TIGR02072 907238003444 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238003445 S-adenosylmethionine binding site [chemical binding]; other site 907238003446 Preprotein translocase subunit SecG [Intracellular trafficking and secretion]; Region: SecG; COG1314 907238003447 ribosome recycling factor; Reviewed; Region: frr; PRK00083 907238003448 Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are "recycled" and ready for another...; Region: RRF; cd00520 907238003449 hinge region; other site 907238003450 Phosphoribosyl transferase (PRT)-type I domain; Region: PRTases_typeI; cd06223 907238003451 active site 907238003452 RDD family; Region: RDD; pfam06271 907238003453 NAD-dependent protein deacetylases, SIR2 family [Transcription]; Region: SIR2; COG0846 907238003454 SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which...; Region: SIRT5_Af1_CobB; cd01412 907238003455 NAD+ binding site [chemical binding]; other site 907238003456 substrate binding site [chemical binding]; other site 907238003457 Zn binding site [ion binding]; other site 907238003458 NADH dehydrogenase subunit A; Validated; Region: PRK08489 907238003459 NADH dehydrogenase subunit B; Validated; Region: PRK06411 907238003460 NADH dehydrogenase subunit C; Provisional; Region: PRK08491 907238003461 NADH (or F420H2) dehydrogenase, subunit C; Region: NuoC_fam; TIGR01961 907238003462 NADH dehydrogenase subunit D; Validated; Region: PRK06075 907238003463 NADH dehydrogenase I, D subunit; Region: NuoD; TIGR01962 907238003464 NADH dehydrogenase subunit G; Validated; Region: PRK08493 907238003465 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis...; Region: fer2; cd00207 907238003466 catalytic loop [active] 907238003467 iron binding site [ion binding]; other site 907238003468 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; Region: NADH-G_4Fe-4S_3; pfam10588 907238003469 Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and...; Region: Molybdopterin-Binding; cl09928 907238003470 molybdopterin cofactor binding site; other site 907238003471 Domain of unknown function (DUF4350); Region: DUF4350; pfam14258 907238003472 NADH:ubiquinone oxidoreductase subunit H; Provisional; Region: PRK06076 907238003473 Formate hydrogenlyase subunit 4 [Energy production and conversion]; Region: HyfC; COG0650 907238003474 NADH-quinone oxidoreductase, chain I; Region: NuoI; TIGR01971 907238003475 4Fe-4S binding domain; Region: Fer4; cl02805 907238003476 4Fe-4S binding domain; Region: Fer4; pfam00037 907238003477 NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]; Region: NuoJ; COG0839 907238003478 NADH dehydrogenase subunit J; Provisional; Region: PRK06433 907238003479 NADH:ubiquinone oxidoreductase subunit K; Validated; Region: PRK05715 907238003480 NADH:ubiquinone oxidoreductase subunit L; Reviewed; Region: PRK06590 907238003481 NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus; Region: Oxidored_q1_N; pfam00662 907238003482 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 907238003483 NADH:ubiquinone oxidoreductase subunit M; Reviewed; Region: PRK05846 907238003484 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 907238003485 proton-translocating NADH-quinone oxidoreductase, chain N; Region: NDH_I_N; TIGR01770 907238003486 NADH-Ubiquinone/plastoquinone (complex I), various chains; Region: Oxidored_q1; pfam00361 907238003487 outer membrane assembly lipoprotein YfiO; Region: OM_YfiO; TIGR03302 907238003488 Phosphomannomutase [Carbohydrate transport and metabolism]; Region: {ManB}; COG1109 907238003489 The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a...; Region: PMM_PGM; cd03089 907238003490 active site 907238003491 substrate binding site [chemical binding]; other site 907238003492 metal binding site [ion binding]; metal-binding site 907238003493 Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both...; Region: Tryptophan_synthase_alpha; cd04724 907238003494 substrate binding site [chemical binding]; other site 907238003495 active site 907238003496 catalytic residues [active] 907238003497 heterodimer interface [polypeptide binding]; other site 907238003498 tryptophan synthase, beta subunit; Region: trpB; TIGR00263 907238003499 Tryptophan synthase-beta: Trptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to...; Region: Trp-synth_B; cd06446 907238003500 pyridoxal 5'-phosphate binding site [chemical binding]; other site 907238003501 catalytic residue [active] 907238003502 bifunctional indole-3-glycerol phosphate synthase/phosphoribosylanthranilate isomerase; Provisional; Region: PRK09427 907238003503 Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the...; Region: IGPS; cd00331 907238003504 active site 907238003505 ribulose/triose binding site [chemical binding]; other site 907238003506 phosphate binding site [ion binding]; other site 907238003507 substrate (anthranilate) binding pocket [chemical binding]; other site 907238003508 product (indole) binding pocket [chemical binding]; other site 907238003509 Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are...; Region: PRAI; cd00405 907238003510 active site 907238003511 Glycosyl transferase family, helical bundle domain; Region: Glycos_trans_3N; pfam02885 907238003512 anthranilate phosphoribosyltransferase; Region: trpD; TIGR01245 907238003513 Glycosyl transferase family, a/b domain; Region: Glycos_transf_3; pfam00591 907238003514 Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase; Region: GATase1_Anthranilate_Synthase; cd01743 907238003515 Glutamine amidotransferase class-I; Region: GATase; pfam00117 907238003516 glutamine binding [chemical binding]; other site 907238003517 catalytic triad [active] 907238003518 anthranilate synthase component I, proteobacterial subset; Region: trpE_proteo; TIGR00565 907238003519 Anthranilate synthase component I, N terminal region; Region: Anth_synt_I_N; pfam04715 907238003520 chorismate binding enzyme; Region: Chorismate_bind; pfam00425 907238003521 ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]; Region: RfaF; COG0859 907238003522 Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate...; Region: Glycosyltransferase_GTB_type; cl10013 907238003523 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 907238003524 active site 907238003525 motif I; other site 907238003526 Predicted phosphatases [General function prediction only]; Region: Gph; COG0546 907238003527 motif II; other site 907238003528 Uncharacterized conserved protein [Function unknown]; Region: COG2353 907238003529 thiaminase II; Region: salvage_TenA; TIGR04306 907238003530 Nicotinamide mononucleotide transporter [Coenzyme metabolism]; Region: PnuC; COG3201 907238003531 Thiamine pyrophosphokinase; Region: TPK; cd07995 907238003532 thiamine pyrophosphokinase; Region: thi_PPkinase; TIGR01378 907238003533 active site 907238003534 dimerization interface [polypeptide binding]; other site 907238003535 thiamine binding site [chemical binding]; other site 907238003536 Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]; Region: RplQ; COG0203 907238003537 N-terminal domain of the Alpha subunit of Bacterial RNA polymerase; Region: RNAP_alpha_NTD; cd06928 907238003538 alphaNTD homodimer interface [polypeptide binding]; other site 907238003539 DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type; Region: rpoA; TIGR02027 907238003540 alphaNTD - beta interaction site [polypeptide binding]; other site 907238003541 alphaNTD - beta' interaction site [polypeptide binding]; other site 907238003542 Bacterial RNA polymerase, alpha chain C terminal domain; Region: RNA_pol_A_CTD; pfam03118 907238003543 30S ribosomal protein S4; Validated; Region: rpsD; PRK05327 907238003544 Ribosomal protein S4/S9 N-terminal domain; Region: Ribosomal_S4; pfam00163 907238003545 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 907238003546 RNA binding surface [nucleotide binding]; other site 907238003547 30S ribosomal protein S11; Validated; Region: PRK05309 907238003548 30S ribosomal protein S13; Validated; Region: rpsM; PRK05179 907238003549 30S ribosomal protein S13; Region: bact_S13; TIGR03631 907238003550 Ribosomal protein L36; Region: Ribosomal_L36; cl00380 907238003551 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the...; Region: S1_IF1; cd04451 907238003552 rRNA binding site [nucleotide binding]; other site 907238003553 predicted 30S ribosome binding site; other site 907238003554 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides; Region: MetAP1; cd01086 907238003555 active site 907238003556 preprotein translocase subunit SecY; Reviewed; Region: secY; PRK09204 907238003557 SecY translocase; Region: SecY; pfam00344 907238003558 50S ribosomal protein L15; Reviewed; Region: rplO; PRK05592 907238003559 ribosomal protein S5, bacterial/organelle type; Region: rpsE_bact; TIGR01021 907238003560 Ribosomal protein S5, N-terminal domain; Region: Ribosomal_S5; pfam00333 907238003561 Ribosomal protein S5, C-terminal domain; Region: Ribosomal_S5_C; pfam03719 907238003562 Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA...; Region: Ribosomal_L18_L5e; cd00432 907238003563 23S rRNA interface [nucleotide binding]; other site 907238003564 5S rRNA interface [nucleotide binding]; other site 907238003565 L27 interface [polypeptide binding]; other site 907238003566 L5 interface [polypeptide binding]; other site 907238003567 50S ribosomal protein L6; Validated; Region: rplF; PRK05498 907238003568 Ribosomal protein L6; Region: Ribosomal_L6; pfam00347 907238003569 30S ribosomal protein S8; Validated; Region: rpsH; PRK00136 907238003570 30S ribosomal protein S14; Reviewed; Region: rpsN; PRK08061 907238003571 50S ribosomal protein L5; Validated; Region: rplE; PRK00010 907238003572 Ribosomal protein L5; Region: Ribosomal_L5; pfam00281 907238003573 ribosomal L5P family C-terminus; Region: Ribosomal_L5_C; pfam00673 907238003574 50S ribosomal protein L24; Reviewed; Region: rplX; PRK00004 907238003575 KOW motif of Ribosomal Protein L26; Region: KOW_RPL26; cd06089 907238003576 RNA binding site [nucleotide binding]; other site 907238003577 50S ribosomal protein L14; Validated; Region: rplN; PRK05483 907238003578 30S ribosomal protein S17; Reviewed; Region: rpsQ; PRK05610 907238003579 Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it...; Region: Ribosomal_L29_HIP; cd00427 907238003580 putative translocon interaction site; other site 907238003581 23S rRNA interface [nucleotide binding]; other site 907238003582 signal recognition particle (SRP54) interaction site; other site 907238003583 L23 interface [polypeptide binding]; other site 907238003584 trigger factor interaction site; other site 907238003585 Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with...; Region: Ribosomal_L16_L10e; cd01433 907238003586 23S rRNA interface [nucleotide binding]; other site 907238003587 5S rRNA interface [nucleotide binding]; other site 907238003588 putative antibiotic binding site [chemical binding]; other site 907238003589 L25 interface [polypeptide binding]; other site 907238003590 L27 interface [polypeptide binding]; other site 907238003591 30S ribosomal protein S3; Reviewed; Region: rpsC; PRK00310 907238003592 K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH...; Region: 30S_S3_KH; cd02412 907238003593 G-X-X-G motif; other site 907238003594 Ribosomal protein S3, C-terminal domain; Region: Ribosomal_S3_C; pfam00189 907238003595 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper...; Region: Ribosomal_L22; cd00336 907238003596 putative translocon binding site; other site 907238003597 protein-rRNA interface [nucleotide binding]; other site 907238003598 30S ribosomal protein S19; Reviewed; Region: rpsS; PRK00357 907238003599 50S ribosomal protein L2; Validated; Region: rplB; PRK09374 907238003600 Ribosomal Proteins L2, RNA binding domain; Region: Ribosomal_L2; pfam00181 907238003601 Ribosomal Proteins L2, C-terminal domain; Region: Ribosomal_L2_C; pfam03947 907238003602 50S ribosomal protein L23; Reviewed; Region: rplW; PRK05738 907238003603 50S ribosomal protein L4; Provisional; Region: rplD; PRK05319 907238003604 50S ribosomal protein L3; Validated; Region: rplC; PRK00001 907238003605 30S ribosomal protein S10; Reviewed; Region: rpsJ; PRK00596 907238003606 Predicted ATPase (AAA+ superfamily) [General function prediction only]; Region: COG1373 907238003607 AAA domain; Region: AAA_14; pfam13173 907238003608 Helix-turn-helix domain; Region: HTH_36; pfam13730 907238003609 bacterial Ribonuclease HII-like; Region: RNase_HII_bacteria_HII_like; cd07182 907238003610 RNA/DNA hybrid binding site [nucleotide binding]; other site 907238003611 active site 907238003612 fumarate hydratase; Reviewed; Region: fumC; PRK00485 907238003613 Class II fumarases; Region: Fumarase_classII; cd01362 907238003614 active site 907238003615 tetramer interface [polypeptide binding]; other site 907238003616 YtkA-like; Region: YtkA; pfam13115 907238003617 Outer membrane efflux protein; Region: OEP; pfam02321 907238003618 Membrane Fusion Protein cluster 2 (function with RND porters); Region: 8a0102; TIGR00999 907238003619 HlyD family secretion protein; Region: HlyD_3; pfam13437 907238003620 Putative silver efflux pump [Inorganic ion transport and metabolism]; Region: COG3696 907238003621 Predicted branched-chain amino acid permeases (azaleucine resistance) [Amino acid transport and metabolism]; Region: AzlD; COG1687 907238003622 AzlC protein; Region: AzlC; cl00570 907238003623 chaperone protein DnaJ; Provisional; Region: PRK14288 907238003624 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 907238003625 HSP70 interaction site [polypeptide binding]; other site 907238003626 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cl03262 907238003627 substrate binding site [polypeptide binding]; other site 907238003628 Zinc finger domain of DnaJ and HSP40; Region: DnaJ_zf; cd10719 907238003629 Zn binding sites [ion binding]; other site 907238003630 C-terminal substrate binding domain of DnaJ and HSP40; Region: DnaJ_C; cd10747 907238003631 dimer interface [polypeptide binding]; other site 907238003632 tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase; Region: trmU; TIGR00420 907238003633 tRNA methyl transferase. This family represents tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs; Region: tRNA_Me_trans; cd01998 907238003634 Ligand Binding Site [chemical binding]; other site 907238003635 DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s; Region: DnaJ; cd06257 907238003636 HSP70 interaction site [polypeptide binding]; other site 907238003637 Nicotinamide/nicotinate mononucleotide adenylyltransferase; Region: NMNAT; cd02165 907238003638 Cytidylyltransferase; Region: CTP_transf_2; pfam01467 907238003639 active site 907238003640 (T/H)XGH motif; other site 907238003641 nickel responsive regulator; Provisional; Region: PRK00630 907238003642 Ribbon-helix-helix protein, copG family; Region: RHH_1; pfam01402 907238003643 NikR C terminal nickel binding domain; Region: NikR_C; pfam08753 907238003644 tonB-system energizer ExbB, group 2; Region: exbB2; TIGR02805 907238003645 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 907238003646 Biopolymer transport protein ExbD/TolR; Region: ExbD; cl00537 907238003647 Periplasmic protein TonB, links inner and outer membranes [Cell envelope biogenesis, outer membrane]; Region: TonB; COG0810 907238003648 Gram-negative bacterial tonB protein; Region: TonB; pfam03544 907238003649 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238003650 Membrane protein TerC, possibly involved in tellurium resistance [Inorganic ion transport and metabolism]; Region: TerC; COG0861 907238003651 Mg2+ and Co2+ transporters [Inorganic ion transport and metabolism]; Region: CorA; COG0598 907238003652 Mg2+ transporter Helicobacter pylori CorA-like subgroup; Region: HpCorA-like; cd12836 907238003653 Cl binding site [ion binding]; other site 907238003654 oligomer interface [polypeptide binding]; other site 907238003655 phosphoglycerate kinase; Provisional; Region: pgk; PRK00073 907238003656 Phosphoglycerate kinase; Region: PGK; pfam00162 907238003657 substrate binding site [chemical binding]; other site 907238003658 hinge regions; other site 907238003659 ADP binding site [chemical binding]; other site 907238003660 catalytic site [active] 907238003661 Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain; Region: Gp_dh_N; pfam00044 907238003662 glyceraldehyde-3-phosphate dehydrogenase, type I; Region: GAPDH-I; TIGR01534 907238003663 Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain; Region: Gp_dh_C; pfam02800 907238003664 Family 1 of Uracil-DNA glycosylase (UDG) enzymes; Region: UDG_F1; cd10027 907238003665 ligand binding site [chemical binding]; other site 907238003666 active site 907238003667 UGI interface [polypeptide binding]; other site 907238003668 catalytic site [active] 907238003669 Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like; Region: LPLAT_AGPAT-like; cd07989 907238003670 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid metabolism]; Region: PlsC; COG0204 907238003671 putative acyl-acceptor binding pocket; other site 907238003672 C-terminal processing peptidase family S41; Region: Peptidase_S41; cl02526 907238003673 C-terminal peptidase (prc); Region: prc; TIGR00225 907238003674 PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for...; Region: PDZ_CTP_protease; cd00988 907238003675 protein binding site [polypeptide binding]; other site 907238003676 C-terminal processing peptidase; serine protease family S41; Region: Peptidase_S41_CPP; cd07560 907238003677 Catalytic dyad [active] 907238003678 Predicted helicase [General function prediction only]; Region: COG4889 907238003679 Predicted helicase [General function prediction only]; Region: COG4889 907238003680 nicotinate-nucleotide pyrophosphorylase; Provisional; Region: PRK05848 907238003681 Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with...; Region: QPRTase; cd01572 907238003682 dimerization interface [polypeptide binding]; other site 907238003683 active site 907238003684 Quinolinate synthetase A protein; Region: NadA; cl00420 907238003685 phosphatidylserine decarboxylase; Provisional; Region: PRK03934 907238003686 prenyltransferase; Reviewed; Region: ubiA; PRK12874 907238003687 UbiA prenyltransferase family; Region: UbiA; pfam01040 907238003688 Predicted membrane metal-binding protein [General function prediction only]; Region: ComEC; COG0658 907238003689 Competence protein; Region: Competence; pfam03772 907238003690 replicative DNA helicase; Provisional; Region: PRK08506 907238003691 DnaB-like helicase N terminal domain; Region: DnaB; pfam00772 907238003692 DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a...; Region: DnaB_C; cd00984 907238003693 Walker A motif; other site 907238003694 ATP binding site [chemical binding]; other site 907238003695 Walker B motif; other site 907238003696 DNA binding loops [nucleotide binding] 907238003697 yjeF N-terminal region; Region: yjeF_nterm; TIGR00197 907238003698 B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily; Region: YXKO-related; cd01171 907238003699 putative substrate binding site [chemical binding]; other site 907238003700 putative ATP binding site [chemical binding]; other site 907238003701 Signal transduction histidine kinase [Signal transduction mechanisms]; Region: BaeS; COG0642 907238003702 His Kinase A (phospho-acceptor) domain; Region: HisKA; pfam00512 907238003703 dimer interface [polypeptide binding]; other site 907238003704 phosphorylation site [posttranslational modification] 907238003705 Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins; Region: HATPase_c; cd00075 907238003706 ATP binding site [chemical binding]; other site 907238003707 Mg2+ binding site [ion binding]; other site 907238003708 G-X-G motif; other site 907238003709 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain [Signal transduction mechanisms / Transcription]; Region: OmpR; COG0745 907238003710 Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; Region: REC; cd00156 907238003711 active site 907238003712 phosphorylation site [posttranslational modification] 907238003713 intermolecular recognition site; other site 907238003714 dimerization interface [polypeptide binding]; other site 907238003715 Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and...; Region: trans_reg_C; cd00383 907238003716 DNA binding site [nucleotide binding] 907238003717 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907238003718 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238003719 DNA modification methylase [DNA replication, recombination, and repair]; Region: COG0863 907238003720 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238003721 potential frameshift: common BLAST hit: gi|308185151|ref|YP_003929284.1| adenine-specific DNA methylase 907238003722 DEAD-like helicases superfamily; Region: DEXDc; smart00487 907238003723 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 907238003724 ATP binding site [chemical binding]; other site 907238003725 putative Mg++ binding site [ion binding]; other site 907238003726 Cell shape-determining protein [Cell envelope biogenesis, outer membrane]; Region: MreC; COG1792 907238003727 rod shape-determining protein MreC; Region: MreC; pfam04085 907238003728 rod shape-determining protein MreB; Provisional; Region: PRK13927 907238003729 MreB and similar proteins; Region: MreB_like; cd10225 907238003730 nucleotide binding site [chemical binding]; other site 907238003731 Mg binding site [ion binding]; other site 907238003732 putative protofilament interaction site [polypeptide binding]; other site 907238003733 RodZ interaction site [polypeptide binding]; other site 907238003734 endopeptidase Clp ATP-binding regulatory subunit (clpX); Region: clpX; TIGR00382 907238003735 ClpX C4-type zinc finger; Region: zf-C4_ClpX; smart00994 907238003736 Magnesium chelatase, subunit ChlI; Region: Mg_chelatase; pfam01078 907238003737 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238003738 Walker A motif; other site 907238003739 ATP binding site [chemical binding]; other site 907238003740 Walker B motif; other site 907238003741 C-terminal, D2-small domain, of ClpB protein; Region: ClpB_D2-small; smart01086 907238003742 Acyl-[acyl carrier protein]; Region: LpxA; COG1043 907238003743 UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic...; Region: LbH_UDP-GlcNAc_AT; cd03351 907238003744 active site 907238003745 FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid...; Region: FabZ; cd01288 907238003746 flagellar assembly protein FliW; Provisional; Region: PRK13282 907238003747 DNA uptake lipoprotein [General function prediction only]; Region: ComL; COG4105 907238003748 ATP-dependent protease La; Region: lon; TIGR00763 907238003749 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238003750 Walker A motif; other site 907238003751 ATP binding site [chemical binding]; other site 907238003752 Walker B motif; other site 907238003753 arginine finger; other site 907238003754 Lon protease (S16) C-terminal proteolytic domain; Region: Lon_C; pfam05362 907238003755 prephenate dehydrogenase; Validated; Region: PRK08507 907238003756 Prephenate dehydrogenase; Region: PDH; pfam02153 907238003757 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]; Region: NUC1; COG1864 907238003758 DNA/RNA non-specific endonuclease; Region: Endonuclease_NS; smart00892 907238003759 active site 907238003760 substrate binding site [chemical binding]; other site 907238003761 Mg2+ binding site [ion binding]; other site 907238003762 Type III restriction/modification enzyme methylation subunit; Region: TypeIII_RM_meth; pfam12564 907238003763 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238003764 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907238003765 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238003766 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3421 907238003767 Type III restriction enzyme, res subunit; Region: ResIII; pfam04851 907238003768 ATP binding site [chemical binding]; other site 907238003769 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cl17251 907238003770 putative Mg++ binding site [ion binding]; other site 907238003771 biotin synthase; Provisional; Region: PRK08508 907238003772 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238003773 FeS/SAM binding site; other site 907238003774 Biotin and Thiamin Synthesis associated domain; Region: BATS; pfam06968 907238003775 YihY family inner membrane protein; Region: yihY_not_rbn; TIGR00765 907238003776 potential protein location (hypothetical protein HPIN_07290 [Helicobacter pylori India7]) that overlaps RNA (5S ribosomal RNA) 907238003777 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907238003778 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238003779 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238003780 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907238003781 7-cyano-7-deazaguanine reductase; Region: QueF-II; TIGR03139 907238003782 Uncharacterized homolog of plant Iojap protein [Function unknown]; Region: COG0799 907238003783 tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]; Region: MiaA; COG0324 907238003784 tRNA dimethylallyltransferase; Region: miaA; TIGR00174 907238003785 Lipopolysaccharide biosynthesis proteins, LPS:glycosyltransferases [Cell envelope biogenesis, outer membrane]; Region: RfaJ; COG1442 907238003786 Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold; Region: Glyco_tranf_GTA_type; cl11394 907238003787 active site 907238003788 potential frameshift: common BLAST hit: gi|188528326|ref|YP_001911013.1| putative type II methylase protein 907238003789 FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in...; Region: FIG; cl00289 907238003790 active site 907238003791 Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose...; Region: RPE; cd00429 907238003792 ribulose-phosphate 3-epimerase; Region: rpe; TIGR01163 907238003793 substrate binding site [chemical binding]; other site 907238003794 hexamer interface [polypeptide binding]; other site 907238003795 metal binding site [ion binding]; metal-binding site 907238003796 DNA polymerase III subunit epsilon; Provisional; Region: PRK08517 907238003797 DEDDh 3'-5' exonuclease domain family; Region: DEDDh; cd06127 907238003798 active site 907238003799 catalytic site [active] 907238003800 substrate binding site [chemical binding]; other site 907238003801 potential frameshift: common BLAST hit: gi|208435411|ref|YP_002267077.1| cysteine-rich protein C 907238003802 Domain of unknown function (DUF814); Region: DUF814; pfam05670 907238003803 ATPase involved in DNA repair [DNA replication, recombination, and repair]; Region: RecN; COG0497 907238003804 ATP-binding cassette transporter nucleotide-binding domain; Region: ABC_ATPase; cl17201 907238003805 Walker A/P-loop; other site 907238003806 ATP binding site [chemical binding]; other site 907238003807 Q-loop/lid; other site 907238003808 ATP-binding cassette domain of RecN; Region: ABC_RecN; cd03241 907238003809 ABC transporter signature motif; other site 907238003810 Walker B; other site 907238003811 D-loop; other site 907238003812 H-loop/switch region; other site 907238003813 NAD kinase [Coenzyme metabolism]; Region: nadF; COG0061 907238003814 ATP-NAD kinase; Region: NAD_kinase; pfam01513 907238003815 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238003816 Protein of unknown function DUF262; Region: DUF262; pfam03235 907238003817 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907238003818 Uncharacterized conserved protein [Function unknown]; Region: COG1479 907238003819 Protein of unknown function (DUF1524); Region: DUF1524; pfam07510 907238003820 Alanine dehydrogenase [Amino acid transport and metabolism]; Region: Ald; COG0686 907238003821 Alanine dehydrogenase NAD-binding and catalytic domains; Region: L-AlaDH; cd05305 907238003822 hexamer interface [polypeptide binding]; other site 907238003823 ligand binding site [chemical binding]; other site 907238003824 putative active site [active] 907238003825 NAD(P) binding site [chemical binding]; other site 907238003826 Arginase family; Region: Arginase; cd09989 907238003827 active site 907238003828 Mn binding site [ion binding]; other site 907238003829 oligomer interface [polypeptide binding]; other site 907238003830 Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]; Region: FecA; COG4772 907238003831 TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel; Region: ligand_gated_channel; cd01347 907238003832 N-terminal plug; other site 907238003833 ligand-binding site [chemical binding]; other site 907238003834 Protein of unknown function DUF45; Region: DUF45; pfam01863 907238003835 type I site-specific deoxyribonuclease, HsdR family; Region: hsdR; TIGR00348 907238003836 Type I restriction enzyme R protein N terminus (HSDR_N); Region: HSDR_N; pfam04313 907238003837 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238003838 ATP binding site [chemical binding]; other site 907238003839 putative Mg++ binding site [ion binding]; other site 907238003840 HsdM N-terminal domain; Region: HsdM_N; pfam12161 907238003841 N-6 DNA Methylase; Region: N6_Mtase; pfam02384 907238003842 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238003843 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907238003844 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907238003845 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238003846 Predicted alternative thymidylate synthase [Nucleotide transport and metabolism]; Region: THY1; COG1351 907238003847 glucosamine--fructose-6-phosphate aminotransferase (isomerizing); Region: glmS; TIGR01135 907238003848 Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In...; Region: GFAT; cd00714 907238003849 glutaminase active site [active] 907238003850 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_1; cd05008 907238003851 dimer interface [polypeptide binding]; other site 907238003852 active site 907238003853 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal...; Region: SIS_GlmS_GlmD_2; cd05009 907238003854 dimer interface [polypeptide binding]; other site 907238003855 active site 907238003856 Protein of unknown function (DUF2443); Region: DUF2443; pfam10398 907238003857 Phosphorylase superfamily; Region: PNP_UDP_1; cl00303 907238003858 chromosomal replication initiator protein DnaA; Region: DnaA; TIGR00362 907238003859 The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC; Region: AAA; cd00009 907238003860 Walker A motif; other site 907238003861 ATP binding site [chemical binding]; other site 907238003862 Walker B motif; other site 907238003863 arginine finger; other site 907238003864 C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple...; Region: Bac_DnaA_C; cd06571 907238003865 DnaA box-binding interface [nucleotide binding]; other site 907238003866 Human Ape1-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases; Region: Ape1-like_AP-endo; cd09087 907238003867 active site 907238003868 putative catalytic site [active] 907238003869 DNA binding site [nucleotide binding] 907238003870 putative phosphate binding site [ion binding]; other site 907238003871 metal binding site A [ion binding]; metal-binding site 907238003872 AP binding site [nucleotide binding]; other site 907238003873 metal binding site B [ion binding]; metal-binding site 907238003874 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238003875 ATP-dependent DNA helicase RecG; Region: recG; TIGR00643 907238003876 RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a...; Region: RecG_wedge_OBF; cd04488 907238003877 ssDNA binding site; other site 907238003878 generic binding surface II; other site 907238003879 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238003880 ATP binding site [chemical binding]; other site 907238003881 putative Mg++ binding site [ion binding]; other site 907238003882 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 907238003883 nucleotide binding region [chemical binding]; other site 907238003884 ATP-binding site [chemical binding]; other site 907238003885 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907238003886 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238003887 DNA methylase; Region: N6_N4_Mtase; pfam01555 907238003888 Adenine specific DNA methylase Mod [DNA replication, recombination, and repair]; Region: COG2189 907238003889 Restriction endonuclease [Defense mechanisms]; Region: COG3587 907238003890 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238003891 ATP binding site [chemical binding]; other site 907238003892 putative Mg++ binding site [ion binding]; other site 907238003893 potential frameshift: common BLAST hit: gi|15612474|ref|NP_224127.1| putative type II DNA modification enzyme (methyltransferase) 907238003894 transcription elongation factor NusA; Provisional; Region: nusA; PRK12328 907238003895 NusA N-terminal domain; Region: NusA_N; pfam08529 907238003896 S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three...; Region: S1_NusA; cd04455 907238003897 RNA binding site [nucleotide binding]; other site 907238003898 homodimer interface [polypeptide binding]; other site 907238003899 NusA-like KH domain; Region: KH_5; pfam13184 907238003900 NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of...; Region: NusA_KH; cd02134 907238003901 G-X-X-G motif; other site 907238003902 Selenocysteine synthase [seryl-tRNASer selenium transferase] [Amino acid transport and metabolism]; Region: SelA; COG1921 907238003903 L-seryl-tRNA selenium transferase; Region: SelA; pfam03841 907238003904 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 907238003905 Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20)...; Region: OM_channels; cl17244 907238003906 TonB-dependent Receptor Plug Domain; Region: Plug; pfam07715 907238003907 FolB domain; Region: folB_dom; TIGR00526 907238003908 active site 907238003909 acyl-phosphate glycerol 3-phosphate acyltransferase; Region: TIGR00023 907238003910 cytochrome c oxidase accessory protein FixG; Region: ccoG_rdxA_fixG; TIGR02745 907238003911 4Fe-4S binding domain; Region: Fer4_5; pfam12801 907238003912 Ubp3 associated protein Bre5; Region: Bre5; pfam11614 907238003913 Saccharopine dehydrogenase and related proteins [Amino acid transport and metabolism]; Region: LYS9; COG1748 907238003914 NAD(P) binding domain of amino acid dehydrogenase-like proteins; Region: NAD_bind_amino_acid_DH; cl17226 907238003915 NAD(P) binding pocket [chemical binding]; other site 907238003916 sodium--glutamate symport carrier (gltS); Region: gltS; TIGR00210 907238003917 Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the...; Region: Riboflavin_deaminase-reductase; cd01284 907238003918 catalytic motif [active] 907238003919 Zn binding site [ion binding]; other site 907238003920 Pyrimidine reductase, riboflavin biosynthesis [Coenzyme metabolism]; Region: RibD; COG1985 907238003921 RibD C-terminal domain; Region: RibD_C; cl17279 907238003922 Predicted O-methyltransferase [General function prediction only]; Region: COG4123 907238003923 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238003924 Putative metal-binding domain of cation transport ATPase; Region: ATPase-cat_bd; pfam12156 907238003925 Cation transport ATPase [Inorganic ion transport and metabolism]; Region: ZntA; COG2217 907238003926 Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain...; Region: HMA; cd00371 907238003927 metal-binding site [ion binding] 907238003928 E1-E2 ATPase; Region: E1-E2_ATPase; pfam00122 907238003929 Soluble P-type ATPase [General function prediction only]; Region: COG4087 907238003930 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3399 907238003931 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238003932 AlwI restriction endonuclease; Region: RE_AlwI; pfam09491 907238003933 Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group...; Region: Cyt_C5_DNA_methylase; cd00315 907238003934 C-5 cytosine-specific DNA methylase; Region: DNA_methylase; pfam00145 907238003935 cofactor binding site; other site 907238003936 DNA binding site [nucleotide binding] 907238003937 substrate interaction site [chemical binding]; other site 907238003938 Predicted permeases [General function prediction only]; Region: COG0795 907238003939 Predicted permease YjgP/YjgQ family; Region: YjgP_YjgQ; pfam03739 907238003940 Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through...; Region: PTH; cd00462 907238003941 putative active site [active] 907238003942 catalytic residue [active] 907238003943 ribosomal protein L25, Ctc-form; Region: ctc_TL5; TIGR00731 907238003944 Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain; Region: Ribosomal_L25_TL5_CTC; cd00495 907238003945 5S rRNA interface [nucleotide binding]; other site 907238003946 CTC domain interface [polypeptide binding]; other site 907238003947 L16 interface [polypeptide binding]; other site 907238003948 Transaldolase-like proteins from plants and bacteria; Region: Transaldolase_like; cd00955 907238003949 putative active site [active] 907238003950 transaldolase; Provisional; Region: PRK03903 907238003951 catalytic residue [active] 907238003952 UDP-N-acetylmuramyl-tripeptide synthetase; Region: murE; TIGR01085 907238003953 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907238003954 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907238003955 NifU-like domain; Region: NifU; pfam01106 907238003956 Phosphate/sulphate permeases [Inorganic ion transport and metabolism]; Region: PitA; COG0306 907238003957 Phosphate transporter family; Region: PHO4; pfam01384 907238003958 Hemolysins and related proteins containing CBS domains [General function prediction only]; Region: TlyC; COG1253 907238003959 Domain of unknown function DUF21; Region: DUF21; pfam01595 907238003960 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in...; Region: CBS_pair_CorC_HlyC_assoc; cd04590 907238003961 Transporter associated domain; Region: CorC_HlyC; smart01091 907238003962 Outer membrane protein [Cell envelope biogenesis, outer membrane / Intracellular trafficking and secretion]; Region: TolC; COG1538 907238003963 Biotin-lipoyl like; Region: Biotin_lipoyl_2; pfam13533 907238003964 HlyD family secretion protein; Region: HlyD_3; pfam13437 907238003965 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 907238003966 ABC-2 type transporter; Region: ABC2_membrane; cl17235 907238003967 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 907238003968 ABC-2 family transporter protein; Region: ABC2_membrane_3; pfam12698 907238003969 ABC-2 type transporter; Region: ABC2_membrane; pfam01061 907238003970 uncharacterized protein, YigZ family; Region: IMPACT_YIGZ; TIGR00257 907238003971 Uncharacterized protein family UPF0029; Region: UPF0029; pfam01205 907238003972 Uncharacterized protein family (UPF0093); Region: UPF0093; cl00863 907238003973 Methylase involved in ubiquinone/menaquinone biosynthesis [Coenzyme metabolism]; Region: UbiE; COG2226 907238003974 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238003975 S-adenosylmethionine binding site [chemical binding]; other site 907238003976 exodeoxyribonuclease VII small subunit; Provisional; Region: PRK14065 907238003977 Predicted amidohydrolase [General function prediction only]; Region: COG0388 907238003978 Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes; Region: nitrilase; cd07197 907238003979 active site 907238003980 catalytic triad [active] 907238003981 dimer interface [polypeptide binding]; other site 907238003982 seryl-tRNA synthetase; Provisional; Region: PRK05431 907238003983 Seryl-tRNA synthetase N-terminal domain; Region: Seryl_tRNA_N; pfam02403 907238003984 Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme...; Region: SerRS_core; cd00770 907238003985 dimer interface [polypeptide binding]; other site 907238003986 active site 907238003987 motif 1; other site 907238003988 motif 2; other site 907238003989 motif 3; other site 907238003990 TPR repeat; Region: TPR_11; pfam13414 907238003991 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 907238003992 TPR motif; other site 907238003993 Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]- X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi; Region: TPR; cd00189 907238003994 binding surface 907238003995 TPR motif; other site 907238003996 Superfamily I DNA and RNA helicases [DNA replication, recombination, and repair]; Region: UvrD; COG0210 907238003997 Part of AAA domain; Region: AAA_19; pfam13245 907238003998 Family description; Region: UvrD_C_2; pfam13538 907238003999 flagellar basal body P-ring biosynthesis protein FlgA; Reviewed; Region: flgA; PRK08515 907238004000 flagella basal body P-ring formation protein FlgA; Region: flgA_cterm; TIGR03170 907238004001 3-octaprenyl-4-hydroxybenzoate carboxy-lyase; Provisional; Region: PRK06029 907238004002 Flavoprotein; Region: Flavoprotein; pfam02441 907238004003 Phosphopantetheine adenylyltransferase [Coenzyme metabolism]; Region: CoaD; COG0669 907238004004 Phosphopantetheine adenylyltransferase; Region: PPAT; cd02163 907238004005 active site 907238004006 (T/H)XGH motif; other site 907238004007 thymidylate kinase; Validated; Region: tmk; PRK00698 907238004008 Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step...; Region: TMPK; cd01672 907238004009 TMP-binding site; other site 907238004010 ATP-binding site [chemical binding]; other site 907238004011 Predicted amidophosphoribosyltransferases [General function prediction only]; Region: ComFC; COG1040 907238004012 Type I restriction-modification system methyltransferase subunit [Defense mechanisms]; Region: HsdM; COG0286 907238004013 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238004014 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238004015 DNA polymerase I; Region: pola; TIGR00593 907238004016 PIN domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: PIN_53EXO; cd09859 907238004017 active site 907238004018 metal binding site 1 [ion binding]; metal-binding site 907238004019 putative 5' ssDNA interaction site; other site 907238004020 metal binding site 3; metal-binding site 907238004021 metal binding site 2 [ion binding]; metal-binding site 907238004022 H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs; Region: H3TH_53EXO; cd09898 907238004023 putative DNA binding site [nucleotide binding]; other site 907238004024 putative metal binding site [ion binding]; other site 907238004025 3'-5' exonuclease; Region: 35EXOc; smart00474 907238004026 active site 907238004027 substrate binding site [chemical binding]; other site 907238004028 catalytic site [active] 907238004029 Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication; Region: DNA_pol_A_pol_I_C; cd08637 907238004030 active site 907238004031 DNA binding site [nucleotide binding] 907238004032 catalytic site [active] 907238004033 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238004034 branched-chain amino acid aminotransferase; Provisional; Region: PRK13357 907238004035 BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and...; Region: BCAT_beta_family; cd01557 907238004036 homodimer interface [polypeptide binding]; other site 907238004037 substrate-cofactor binding pocket; other site 907238004038 catalytic residue [active] 907238004039 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238004040 ABC-type transport system involved in resistance to organic solvents, permease component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2B; COG0767 907238004041 conserved hypothetical integral membrane protein; Region: TIGR00056 907238004042 ABC-type transport system involved in resistance to organic solvents, ATPase component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2A; COG1127 907238004043 ATP-binding cassette transport system involved in resistant to organic solvents; Region: ABC_Org_Solvent_Resistant; cd03261 907238004044 Walker A/P-loop; other site 907238004045 ATP binding site [chemical binding]; other site 907238004046 Q-loop/lid; other site 907238004047 ABC transporter signature motif; other site 907238004048 Walker B; other site 907238004049 D-loop; other site 907238004050 H-loop/switch region; other site 907238004051 ABC-type transport system involved in resistance to organic solvents, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]; Region: Ttg2C; COG1463 907238004052 mce related protein; Region: MCE; pfam02470 907238004053 Heat shock protein [Posttranslational modification, protein turnover, chaperones]; Region: HslJ; COG3187 907238004054 Cytochrome c peroxidase [Inorganic ion transport and metabolism]; Region: MauG; COG1858 907238004055 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3; Region: PHP_PolIIIA_DnaE3; cd12113 907238004056 DNA polymerase III subunit alpha; Validated; Region: dnaE; PRK05673 907238004057 active site 907238004058 PHP Thumb interface [polypeptide binding]; other site 907238004059 metal binding site [ion binding]; metal-binding site 907238004060 DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains...; Region: DnaE_OBF; cd04485 907238004061 generic binding surface I; other site 907238004062 generic binding surface II; other site 907238004063 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]; Region: RsuA; COG1187 907238004064 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 907238004065 RNA binding surface [nucleotide binding]; other site 907238004066 Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi); Region: PseudoU_synth; cl00130 907238004067 active site 907238004068 TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox...; Region: TRX_family; cd02947 907238004069 catalytic residues [active] 907238004070 Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]; Region: FlgN; COG3417 907238004071 LPP20 lipoprotein; Region: LPP20; pfam02169 907238004072 Helicobacter outer membrane protein; Region: HP_OMP; pfam01856 907238004073 GTP-binding protein TrmE N-terminus; Region: TrmE_N; pfam10396 907238004074 tRNA modification GTPase TrmE; Region: mnmE_trmE_thdF; TIGR00450 907238004075 Circularly permuted YlqF-related GTPases; Region: YlqF_related_GTPase; cl17249 907238004076 GTP/Mg2+ binding site [chemical binding]; other site 907238004077 G4 box; other site 907238004078 G5 box; other site 907238004079 trmE is a tRNA modification GTPase; Region: trmE; cd04164 907238004080 G1 box; other site 907238004081 G1 box; other site 907238004082 GTP/Mg2+ binding site [chemical binding]; other site 907238004083 Switch I region; other site 907238004084 Switch I region; other site 907238004085 G2 box; other site 907238004086 G2 box; other site 907238004087 Switch II region; other site 907238004088 G3 box; other site 907238004089 G3 box; other site 907238004090 Switch II region; other site 907238004091 G4 box; other site 907238004092 G5 box; other site 907238004093 Catalytic cysteine-containing C-terminus of GTPase, MnmE; Region: GTPase_Cys_C; pfam12631 907238004094 Predicted RNA-binding protein [General function prediction only]; Region: Jag; COG1847 907238004095 membrane protein insertase; Provisional; Region: PRK01318 907238004096 membrane protein insertase, YidC/Oxa1 family, C-terminal domain; Region: yidC_oxa1_cterm; TIGR03592 907238004097 hypothetical protein; Provisional; Region: PRK14374 907238004098 ribonuclease P protein component, eubacterial; Region: rnpA; TIGR00188 907238004099 50S ribosomal protein L34; Reviewed; Region: rpmH; PRK00399 907238004100 Biopolymer transport protein [Intracellular trafficking and secretion]; Region: ExbD; COG0848 907238004101 Biopolymer transport protein ExbD/TolR; Region: ExbD; pfam02472 907238004102 MotA/TolQ/ExbB proton channel family; Region: MotA_ExbB; pfam01618 907238004103 Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs; Region: SmpB; cd09294 907238004104 SmpB-tmRNA interface; other site 907238004105 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional; Region: PRK04181 907238004106 carbon storage regulator; Provisional; Region: PRK00568 907238004107 cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the...; Region: cyclophilin; cd00317 907238004108 active site 907238004109 TIR domain; Region: TIR_2; pfam13676 907238004110 signal peptide peptidase SppA, 36K type; Region: SppA_dom; TIGR00706 907238004111 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad; Region: S49_Sppa_N_C; cd07023 907238004112 tandem repeat interface [polypeptide binding]; other site 907238004113 oligomer interface [polypeptide binding]; other site 907238004114 active site residues [active] 907238004115 formyltetrahydrofolate deformylase; Region: PurU; TIGR00655 907238004116 N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase); Region: ACT_F4HF-DF; cd04875 907238004117 Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain; Region: FMT_core_Formyl-FH4-Hydrolase_C; cd08648 907238004118 putative active site [active] 907238004119 putative substrate binding site [chemical binding]; other site 907238004120 putative cosubstrate binding site; other site 907238004121 catalytic site [active] 907238004122 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238004123 Restriction endonuclease S subunits [Defense mechanisms]; Region: HsdS; COG0732 907238004124 Type I restriction modification DNA specificity domain; Region: Methylase_S; pfam01420 907238004125 16S ribosomal RNA methyltransferase KsgA/Dim1 family protein; Reviewed; Region: ksgA; PRK00274 907238004126 S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy); Region: AdoMet_MTases; cd02440 907238004127 S-adenosylmethionine binding site [chemical binding]; other site 907238004128 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]; Region: COG0595 907238004129 Metallo-beta-lactamase superfamily; Region: Lactamase_B; smart00849 907238004130 RNA-metabolising metallo-beta-lactamase; Region: RMMBL; pfam07521 907238004131 KpsF/GutQ family protein; Region: kpsF; TIGR00393 907238004132 KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose...; Region: SIS_Kpsf; cd05014 907238004133 putative active site [active] 907238004134 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with KpsF/GutQ domains in the API [A5P (D-arabinose 5-phosphate) isomerase] protein. These APIs catalyze the conversion of the pentose pathway...; Region: CBS_pair_KpsF_GutQ_assoc; cd04604 907238004135 ribosomal RNA large subunit methyltransferase N; Provisional; Region: PRK14462 907238004136 Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster; Region: Radical_SAM; cd01335 907238004137 FeS/SAM binding site; other site 907238004138 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized...; Region: S4; cd00165 907238004139 RNA binding surface [nucleotide binding]; other site 907238004140 isoleucyl-tRNA synthetase; Reviewed; Region: ileS; PRK05743 907238004141 nucleotidyl transferase superfamily; Region: nt_trans; cl00015 907238004142 active site 907238004143 HIGH motif; other site 907238004144 nucleotide binding site [chemical binding]; other site 907238004145 catalytic core domain of isoleucyl-tRNA synthetases; Region: IleRS_core; cd00818 907238004146 active site 907238004147 KMSKS motif; other site 907238004148 Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases; Region: Anticodon_Ia_Ile_BEm; cd07960 907238004149 tRNA binding surface [nucleotide binding]; other site 907238004150 anticodon binding site; other site 907238004151 Zinc finger found in FPG and IleRS; Region: zf-FPG_IleRS; pfam06827 907238004152 Type IV secretory pathway, VirB11 components, and related ATPases involved in archaeal flagella biosynthesis [Cell motility and secretion / Intracellular trafficking and secretion]; Region: VirB11; COG0630 907238004153 Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to...; Region: VirB11-like_ATPase; cd01130 907238004154 ATP binding site [chemical binding]; other site 907238004155 Walker A motif; other site 907238004156 hexamer interface [polypeptide binding]; other site 907238004157 Walker B motif; other site 907238004158 flagellum-specific ATP synthase; Validated; Region: fliI; PRK08472 907238004159 Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they...; Region: ATPase_flagellum-secretory_path_III; cd01136 907238004160 Walker A motif/ATP binding site; other site 907238004161 Walker B motif; other site 907238004162 flagellar biosynthesis protein FliQ; Validated; Region: fliQ; PRK05700 907238004163 UDP-N-acetylenolpyruvoylglucosamine reductase; Provisional; Region: murB; PRK13904 907238004164 UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain; Region: MurB_C; pfam02873 907238004165 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 907238004166 DNA breaking-rejoining enzymes, intergrase/recombinases, C-terminal catalytic domain. The tyrosine recombinase/integrase family share the same catalytic domain containing six conserved active site residues. The best-studied members of this diverse family...; Region: INT_REC_C; cd01182 907238004167 active site 907238004168 catalytic residues [active] 907238004169 DNA binding site [nucleotide binding] 907238004170 Int/Topo IB signature motif; other site 907238004171 Type IV secretory pathway, TrbL components [Intracellular trafficking and secretion]; Region: TrbL; COG3846 907238004172 ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]; Region: Soj; COG1192 907238004173 potential frameshift: common BLAST hit: gi|210134648|ref|YP_002301087.1| relaxase 907238004174 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG3041; cl17396 907238004175 elongation factor Ts; Provisional; Region: tsf; PRK09377 907238004176 UBA/TS-N domain; Region: UBA; pfam00627 907238004177 Elongation factor TS; Region: EF_TS; pfam00889 907238004178 Elongation factor TS; Region: EF_TS; pfam00889 907238004179 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of...; Region: RPS2; cd01425 907238004180 rRNA interaction site [nucleotide binding]; other site 907238004181 S8 interaction site; other site 907238004182 putative laminin-1 binding site; other site 907238004183 putative recombination protein RecB; Provisional; Region: PRK13909 907238004184 Family description; Region: UvrD_C_2; pfam13538 907238004185 PD-(D/E)XK nuclease superfamily; Region: PDDEXK_1; pfam12705 907238004186 pH-dependent sodium/proton antiporter; Provisional; Region: nhaA; PRK14856 907238004187 preprotein translocase subunit YajC; Validated; Region: yajC; PRK05585 907238004188 preprotein translocase subunit SecD; Reviewed; Region: secD; PRK05812 907238004189 protein-export membrane protein, SecD/SecF family; Region: 2A0604s01; TIGR00916 907238004190 protein-export membrane protein SecF; Region: 3a0501s07; TIGR00966 907238004191 Protein export membrane protein; Region: SecD_SecF; pfam02355 907238004192 leucyl-tRNA synthetase; Validated; Region: leuS; PRK00390 907238004193 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 907238004194 HIGH motif; other site 907238004195 Leucyl-tRNA synthetase, Domain 2; Region: tRNA-synt_1_2; pfam13603 907238004196 catalytic core domain of leucyl-tRNA synthetases; Region: LeuRS_core; cd00812 907238004197 active site 907238004198 KMSKS motif; other site 907238004199 Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains; Region: Anticodon_Ia_like; cl12020 907238004200 tRNA binding surface [nucleotide binding]; other site 907238004201 anticodon binding site; other site 907238004202 Lipopolysaccharide-assembly; Region: LptE; pfam04390 907238004203 Folylpolyglutamate synthase [Coenzyme metabolism]; Region: FolC; COG0285 907238004204 Mur ligase middle domain; Region: Mur_ligase_M; pfam08245 907238004205 Mur ligase family, glutamate ligase domain; Region: Mur_ligase_C; pfam02875 907238004206 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907238004207 Peptidase family M23; Region: Peptidase_M23; pfam01551 907238004208 Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]; Region: NlpD; COG0739 907238004209 Peptidase family M23; Region: Peptidase_M23; pfam01551 907238004210 Integral membrane protein CcmA involved in cell shape determination [Cell envelope biogenesis, outer membrane]; Region: CcmA; COG1664 907238004211 Polymer-forming cytoskeletal; Region: Bactofilin; pfam04519 907238004212 transcription-repair coupling factor (mfd); Region: mfd; TIGR00580 907238004213 CarD-like/TRCF domain; Region: CarD_TRCF; smart01058 907238004214 DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region; Region: DEXDc; cd00046 907238004215 ATP binding site [chemical binding]; other site 907238004216 putative Mg++ binding site [ion binding]; other site 907238004217 Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may...; Region: HELICc; cd00079 907238004218 nucleotide binding region [chemical binding]; other site 907238004219 ATP-binding site [chemical binding]; other site 907238004220 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli; Region: TRCF; smart00982 907238004221 ubiquinol-cytochrome c reductase, iron-sulfur subunit; Region: Rieske_proteo; TIGR01416 907238004222 Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes; Region: Rieske; cl00938 907238004223 iron-sulfur cluster [ion binding]; other site 907238004224 [2Fe-2S] cluster binding site [ion binding]; other site 907238004225 Cytochrome b subunit of the bc complex [Energy production and conversion]; Region: QcrB; COG1290 907238004226 Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria; Region: Cytochrome_b_N; cd00284 907238004227 intrachain domain interface; other site 907238004228 interchain domain interface [polypeptide binding]; other site 907238004229 heme bH binding site [chemical binding]; other site 907238004230 Qi binding site; other site 907238004231 heme bL binding site [chemical binding]; other site 907238004232 Qo binding site; other site 907238004233 interchain domain interface [polypeptide binding]; other site 907238004234 intrachain domain interface; other site 907238004235 Qi binding site; other site 907238004236 Cytochrome b(C-terminal)/b6/petD; Region: Cytochrom_B_C; pfam00032 907238004237 Qo binding site; other site 907238004238 Cytochrome c1 [Energy production and conversion]; Region: CYT1; COG2857 907238004239 Cytochrome c; Region: Cytochrom_C; pfam00034 907238004240 Cytochrome c; Region: Cytochrom_C; cl11414 907238004241 Cell division protein FtsI/penicillin-binding protein 2 [Cell envelope biogenesis, outer membrane]; Region: FtsI; COG0768 907238004242 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 907238004243 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 907238004244 flagellar hook-basal body protein FliE; Reviewed; Region: fliE; PRK03907 907238004245 flagellar basal body rod protein FlgC; Reviewed; Region: flgC; PRK05681 907238004246 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907238004247 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK05680 907238004248 flagellar basal body rod protein FlgB; Reviewed; Region: flgB; PRK07182 907238004249 Cell cycle protein; Region: FTSW_RODA_SPOVE; pfam01098 907238004250 ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]; Region: FepB; COG0614 907238004251 Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a...; Region: TroA_d; cd01141 907238004252 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]; Region: AhpC; COG0450 907238004253 Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides; Region: PRX_Typ2cys; cd03015 907238004254 dimer interface [polypeptide binding]; other site 907238004255 decamer (pentamer of dimers) interface [polypeptide binding]; other site 907238004256 catalytic triad [active] 907238004257 peroxidatic and resolving cysteines [active] 907238004258 ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]; Region: NlpA; COG1464 907238004259 NLPA lipoprotein; Region: Lipoprotein_9; pfam03180 907238004260 penicillin-binding protein 2; Region: pbp2_mrdA; TIGR03423 907238004261 Penicillin-binding Protein dimerisation domain; Region: PBP_dimer; pfam03717 907238004262 Penicillin binding protein transpeptidase domain; Region: Transpeptidase; pfam00905 907238004263 YihA (EngB) GTPase family; Region: YihA_EngB; cd01876 907238004264 G1 box; other site 907238004265 GTP/Mg2+ binding site [chemical binding]; other site 907238004266 Switch I region; other site 907238004267 G2 box; other site 907238004268 G3 box; other site 907238004269 Switch II region; other site 907238004270 G4 box; other site 907238004271 G5 box; other site 907238004272 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG1934 907238004273 OstA-like protein; Region: OstA; pfam03968 907238004274 Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others; Region: HAD_like; cd01427 907238004275 motif II; other site 907238004276 Lipoproteins [Cell envelope biogenesis, outer membrane]; Region: RlpA; COG0797 907238004277 Rare lipoprotein A (RlpA)-like double-psi beta-barrel; Region: DPBB_1; pfam03330 907238004278 Sporulation related domain; Region: SPOR; pfam05036 907238004279 Lytic Transglycosylase (LT) and Goose Egg White Lysozyme (GEWL) domain. Members include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as, the eukaryotic "goose-type" lysozymes (GEWL). LTs...; Region: LT_GEWL; cd00254 907238004280 N-acetyl-D-glucosamine binding site [chemical binding]; other site 907238004281 catalytic residue [active] 907238004282 Lysine Motif is a small domain involved in binding peptidoglycan; Region: LysM; cd00118 907238004283 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]; Region: COG1099 907238004284 TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity; Region: TatD_DNAse; cd01310 907238004285 active site 907238004286 riboflavin synthase, alpha subunit; Region: ribE; TIGR00187 907238004287 Lumazine binding domain; Region: Lum_binding; pfam00677 907238004288 Lumazine binding domain; Region: Lum_binding; pfam00677 907238004289 flhB C-terminus-related protein; Region: flhB_rel; TIGR00789 907238004290 DL-methionine transporter ATP-binding subunit; Provisional; Region: metN; PRK11153 907238004291 ATP-binding cassette domain of methionine transporter; Region: ABC_MetN_methionine_transporter; cd03258 907238004292 Walker A/P-loop; other site 907238004293 ATP binding site [chemical binding]; other site 907238004294 Q-loop/lid; other site 907238004295 ABC transporter signature motif; other site 907238004296 Walker B; other site 907238004297 D-loop; other site 907238004298 H-loop/switch region; other site 907238004299 NIL domain; Region: NIL; pfam09383 907238004300 ABC-type metal ion transport system, permease component [Inorganic ion transport and metabolism]; Region: AbcD; COG2011 907238004301 Membrane-associated phospholipid phosphatase [Lipid metabolism]; Region: PgpB; COG0671 907238004302 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase; Region: PAP2_like_5; cd03394 907238004303 active site 907238004304 UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N- acetylglucosamine-1-phosphate transferase [Cell envelope biogenesis, outer membrane]; Region: Rfe; COG0472 907238004305 This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which...; Region: GT_MraY_like; cd06912 907238004306 Mg++ binding site [ion binding]; other site 907238004307 putative catalytic motif [active] 907238004308 Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in...; Region: PNPsynthase; cd00003 907238004309 active site 907238004310 hydrophilic channel; other site 907238004311 dimerization interface [polypeptide binding]; other site 907238004312 catalytic residues [active] 907238004313 active site lid [active] 907238004314 4-hydroxythreonine-4-phosphate dehydrogenase; Validated; Region: pdxA; PRK03743 907238004315 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional; Region: pdxA; PRK03946 907238004316 Inactive homolog of metal-dependent proteases, putative molecular chaperone [Posttranslational modification, protein turnover, chaperones]; Region: COG1214; cl17884 907238004317 metallohydrolase, glycoprotease/Kae1 family; Region: gcp_kae1; TIGR00329 907238004318 flagellar basal body rod protein FlgG; Provisional; Region: flgG; PRK12693 907238004319 Flagella basal body rod protein; Region: Flg_bb_rod; pfam00460 907238004320 Flagellar basal body rod FlgEFG protein C-terminal; Region: Flg_bbr_C; pfam06429 907238004321 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 907238004322 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 907238004323 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735 907238004324 hypothetical protein; Provisional; Region: PRK10236 907238004325 Domain of unknown function (DUF3944); Region: DUF3944; pfam13099 907238004326 Uncharacterized protein conserved in bacteria [Function unknown]; Region: COG4735